Created by Bpipe, Mon May 16 11:59:17 EST 2016
Branch 1
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:49 (16.007 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:49 - 2016-5-16 11:15:52 (2.911 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:52 - 2016-5-16 11:16:13 (21.131 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:13 (0.841 seconds) |
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| Execution Time | 2016-5-16 11:16:14 - 2016-5-16 11:16:37 (23.009 seconds) |
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| Execution Time | 2016-5-16 11:16:37 - 2016-5-16 11:16:59 (22.287 seconds) |
Mark Duplicates with PicardTools
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| Execution Time | 2016-5-16 11:16:59 - 2016-5-16 11:17:1 (1.301 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:1 - 2016-5-16 11:17:3 (1.811 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:3 - 2016-5-16 11:17:4 (1.109 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:4 - 2016-5-16 11:17:5 (1.087 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:5 - 2016-5-16 11:17:7 (2.174 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:17:7 (0.989 seconds) |
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| Execution Time | 2016-5-16 11:17:8 (0.889 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:9 - 2016-5-16 11:17:13 (3.651 seconds) |
Collect insert size metrics
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| Commands | 21335 |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:19:44 (2 minutes, 31.072 seconds) |
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| Commands | 21502 |
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| Execution Time | 2016-5-16 11:19:44 (0.035 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Execution Time | 2016-5-16 11:19:44 (0.008 seconds) |
Branch 2
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.274 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.125 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (21.963 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:17 - 2016-5-16 11:16:18 (1.419 seconds) |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:44 (25.610 seconds) |
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| Execution Time | 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.637 seconds) |
Mark Duplicates with PicardTools
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| Execution Time | 2016-5-16 11:17:8 (0.838 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:8 (0.807 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:9 (0.965 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:11 (0.745 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.252 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.156 seconds) |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:17 (2.621 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:17 - 2016-5-16 11:17:44 (26.807 seconds) |
Collect insert size metrics
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| Commands | 21456 |
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| Execution Time | 2016-5-16 11:17:44 - 2016-5-16 11:35:39 (17 minutes, 55.226 seconds) |
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| Commands | 21854 |
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| Execution Time | 2016-5-16 11:35:39 (0.043 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Execution Time | 2016-5-16 11:35:39 (0.012 seconds) |
Branch 3
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.284 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:54 (0.798 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:16 (21.106 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:16 - 2016-5-16 11:16:17 (1.318 seconds) |
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| Execution Time | 2016-5-16 11:16:17 - 2016-5-16 11:16:40 (22.794 seconds) |
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| Execution Time | 2016-5-16 11:16:40 - 2016-5-16 11:17:7 (26.739 seconds) |
Mark Duplicates with PicardTools
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| Execution Time | 2016-5-16 11:17:7 (0.644 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:8 (0.740 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:8 (0.717 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:9 (0.730 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:10 (0.800 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:17:11 (0.308 seconds) |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.029 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:35 (22.311 seconds) |
Collect insert size metrics
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| Commands | 21346 |
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| Execution Time | 2016-5-16 11:17:35 - 2016-5-16 11:21:25 (3 minutes, 50.415 seconds) |
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| Commands | 21544 |
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| Execution Time | 2016-5-16 11:21:25 (0.053 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Execution Time | 2016-5-16 11:21:25 (0.008 seconds) |
Branch 4
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.903 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:54 (0.890 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.570 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:18 (0.972 seconds) |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (25.277 seconds) |
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| Execution Time | 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.294 seconds) |
Mark Duplicates with PicardTools
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| Execution Time | 2016-5-16 11:17:8 (0.745 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:8 (0.658 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:9 (0.675 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:10 (0.775 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.437 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:17:12 (0.986 seconds) |
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| Execution Time | 2016-5-16 11:17:13 (0.919 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:38 (24.174 seconds) |
Collect insert size metrics
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| Commands | 21357 |
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| Execution Time | 2016-5-16 11:17:38 - 2016-5-16 11:23:13 (5 minutes, 34.706 seconds) |
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| Commands | 21580 |
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| Execution Time | 2016-5-16 11:23:13 (0.052 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Execution Time | 2016-5-16 11:23:13 (0.013 seconds) |
Branch 5
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (19.946 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.279 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.714 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.584 seconds) |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (24.368 seconds) |
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| Execution Time | 2016-5-16 11:16:44 - 2016-5-16 11:17:7 (23.851 seconds) |
Mark Duplicates with PicardTools
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| Execution Time | 2016-5-16 11:17:7 (0.685 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:8 (0.709 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:9 (0.731 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:10 (0.729 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:11 (0.471 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:17:11 (0.821 seconds) |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.083 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:37 (23.669 seconds) |
Collect insert size metrics
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| Commands | 21367 |
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| Execution Time | 2016-5-16 11:17:37 - 2016-5-16 11:26:2 (8 minutes, 25.317 seconds) |
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| Commands | 21634 |
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| Execution Time | 2016-5-16 11:26:2 (0.035 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Execution Time | 2016-5-16 11:26:2 (0.009 seconds) |
Branch 6
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.752 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.203 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.884 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:20 (1.299 seconds) |
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| Execution Time | 2016-5-16 11:16:20 - 2016-5-16 11:16:45 (25.114 seconds) |
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| Execution Time | 2016-5-16 11:16:45 - 2016-5-16 11:17:8 (23.000 seconds) |
Mark Duplicates with PicardTools
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| Execution Time | 2016-5-16 11:17:8 (0.725 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:9 (0.924 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:10 (0.849 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:11 (0.752 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.136 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.249 seconds) |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (1.883 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:16 - 2016-5-16 11:17:44 (28.291 seconds) |
Collect insert size metrics
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| Commands | 21444 |
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| Execution Time | 2016-5-16 11:17:44 - 2016-5-16 11:34:20 (16 minutes, 35.496 seconds) |
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| Commands | 21826 |
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| Execution Time | 2016-5-16 11:34:20 (0.032 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Execution Time | 2016-5-16 11:34:20 (0.007 seconds) |
Branch 7
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.731 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:54 (0.773 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (21.627 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:17 - 2016-5-16 11:16:18 (1.298 seconds) |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:43 (24.831 seconds) |
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:16:43 - 2016-5-16 11:17:7 (24.487 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:17:7 (0.691 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.725 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.710 seconds) |
Apply BQSR to input BAM file.
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 - 2016-5-16 11:17:11 (1.028 seconds) |
Compare pre and post base-quality scores from recalibration
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.121 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 (0.955 seconds) |
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.115 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:40 (25.812 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21413 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:40 - 2016-5-16 11:30:7 (12 minutes, 27.021 seconds) |
| Inputs |
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| Commands | 21730 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:30:7 (0.036 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Outputs |
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| Execution Time | 2016-5-16 11:30:7 (0.008 seconds) |
Branch 8
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.253 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.177 seconds) |
Mark Illumina Adapters with PicardTools
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.602 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:18 (0.971 seconds) |
| Inputs |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (24.710 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (24.289 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.748 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.696 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.935 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.027 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.114 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.442 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:15 - 2016-5-16 11:17:17 (2.035 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:17 - 2016-5-16 11:17:46 (29.399 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21462 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:46 - 2016-5-16 11:36:48 (19 minutes, 2.280 seconds) |
| Inputs |
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|---|---|
| Commands | 21881 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:36:48 (0.037 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:36:49 (0.009 seconds) |
Branch 9
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Outputs |
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:55 (21.333 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:15:56 (1.634 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:15:56 - 2016-5-16 11:16:19 (23.016 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:21 (1.215 seconds) |
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:16:21 - 2016-5-16 11:16:44 (23.476 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:44 - 2016-5-16 11:17:7 (23.241 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:7 (0.871 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.769 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.629 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.737 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.153 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.186 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.022 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:41 (26.432 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21388 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:41 - 2016-5-16 11:27:33 (9 minutes, 52.736 seconds) |
| Inputs |
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|---|---|
| Commands | 21670 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:27:33 (0.032 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:27:33 (0.008 seconds) |
Branch 10
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.769 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.034 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.426 seconds) |
Create merged BAM alignment from unmapped BAM file
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.053 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:43 (24.714 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.988 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.789 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.664 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.701 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.985 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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|---|---|
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:13 (1.458 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 (0.855 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (2.114 seconds) |
Collect alignment summary statistics
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:16 - 2016-5-16 11:17:43 (27.275 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21461 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:43 - 2016-5-16 11:36:18 (18 minutes, 34.704 seconds) |
| Inputs |
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|---|---|
| Commands | 21862 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:36:18 (0.034 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:36:18 (0.009 seconds) |
Branch 11
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:47 (14.577 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:47 (0.101 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:48 - 2016-5-16 11:16:6 (18.801 seconds) |
Create merged BAM alignment from unmapped BAM file
| Inputs |
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|---|---|
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:7 - 2016-5-16 11:16:12 (4.837 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:12 - 2016-5-16 11:16:34 (22.930 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:35 - 2016-5-16 11:17:0 (25.989 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:1 - 2016-5-16 11:17:3 (2.014 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:3 - 2016-5-16 11:17:5 (1.794 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:5 - 2016-5-16 11:17:6 (1.229 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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|---|---|
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:6 - 2016-5-16 11:17:7 (1.446 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:7 - 2016-5-16 11:17:8 (1.209 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 - 2016-5-16 11:17:10 (1.250 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.677 seconds) |
Collect alignment summary statistics
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:26 (14.783 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21337 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:26 - 2016-5-16 11:20:26 (3 minutes, 0.645 seconds) |
| Inputs |
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|---|---|
| Commands | 21517 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:20:26 (0.034 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:20:26 (0.009 seconds) |
Branch 12
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.663 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:56 (1.204 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:56 - 2016-5-16 11:16:18 (21.862 seconds) |
Create merged BAM alignment from unmapped BAM file
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.504 seconds) |
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:46 (27.131 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:47 - 2016-5-16 11:17:9 (22.614 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.832 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:10 (0.731 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.028 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 (0.945 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.239 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:17 (2.446 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:17 - 2016-5-16 11:17:19 (2.446 seconds) |
Collect alignment summary statistics
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:19 - 2016-5-16 11:17:45 (25.791 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21469 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:45 - 2016-5-16 11:37:55 (20 minutes, 9.177 seconds) |
| Inputs |
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|---|---|
| Commands | 21910 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:37:55 (0.035 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:37:55 (0.008 seconds) |
Branch 13
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.237 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.157 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (21.543 seconds) |
Create merged BAM alignment from unmapped BAM file
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:17 - 2016-5-16 11:16:18 (1.310 seconds) |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:43 (25.146 seconds) |
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| Execution Time | 2016-5-16 11:16:43 - 2016-5-16 11:17:7 (24.264 seconds) |
Mark Duplicates with PicardTools
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| Execution Time | 2016-5-16 11:17:8 (0.757 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:8 (0.828 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:9 (0.699 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:10 (0.845 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:11 (0.907 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:17:12 (0.926 seconds) |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.089 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:41 (27.209 seconds) |
Collect insert size metrics
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| Commands | 21419 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:41 - 2016-5-16 11:31:37 (13 minutes, 55.857 seconds) |
| Inputs |
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| Commands | 21766 |
| Outputs |
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| Execution Time | 2016-5-16 11:31:37 (0.034 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Execution Time | 2016-5-16 11:31:37 (0.008 seconds) |
Branch 14
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.601 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:54 (0.824 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (21.611 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:17 - 2016-5-16 11:16:18 (1.602 seconds) |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:41 (23.048 seconds) |
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| Execution Time | 2016-5-16 11:16:41 - 2016-5-16 11:17:6 (24.521 seconds) |
Mark Duplicates with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:17:6 (0.963 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:7 (0.741 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.959 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:9 (0.688 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:10 - 2016-5-16 11:17:11 (1.173 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:17:11 (0.979 seconds) |
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| Outputs |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.155 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:37 (24.410 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21364 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:37 - 2016-5-16 11:23:51 (6 minutes, 13.767 seconds) |
| Inputs |
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| Commands | 21589 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:23:51 (0.037 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Outputs |
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| Execution Time | 2016-5-16 11:23:51 (0.010 seconds) |
Branch 15
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (19.791 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.107 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (22.484 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:17 - 2016-5-16 11:16:18 (1.122 seconds) |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:43 (24.531 seconds) |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:43 - 2016-5-16 11:17:6 (22.909 seconds) |
Mark Duplicates with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:17:6 - 2016-5-16 11:17:7 (1.457 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:7 (0.714 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:8 (0.833 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.770 seconds) |
Compare pre and post base-quality scores from recalibration
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.821 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.538 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.083 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:35 (22.487 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21351 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:35 - 2016-5-16 11:21:24 (3 minutes, 48.733 seconds) |
| Inputs |
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| Commands | 21538 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:21:24 (0.038 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:21:24 (0.008 seconds) |
Branch 16
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:55 (20.585 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:55 (0.782 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:20 (24.768 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:20 - 2016-5-16 11:16:22 (2.330 seconds) |
| Inputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:22 - 2016-5-16 11:16:46 (23.849 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:46 - 2016-5-16 11:17:8 (21.821 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.794 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.532 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.803 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.870 seconds) |
Compare pre and post base-quality scores from recalibration
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.168 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 (0.941 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:15 (1.657 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:15 - 2016-5-16 11:17:40 (24.641 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21422 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:40 - 2016-5-16 11:31:23 (13 minutes, 42.721 seconds) |
| Inputs |
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|---|---|
| Commands | 21760 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:31:23 (0.052 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:31:23 (0.012 seconds) |
Branch 17
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.582 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 (0.945 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:19 (23.261 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:20 (1.778 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:20 - 2016-5-16 11:16:46 (25.667 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:46 - 2016-5-16 11:17:9 (22.278 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.743 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.727 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.812 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.623 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 (0.778 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.273 seconds) |
| Inputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:17 (2.605 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:17 - 2016-5-16 11:17:43 (26.728 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21415 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:44 - 2016-5-16 11:30:30 (12 minutes, 46.603 seconds) |
| Inputs |
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| Commands | 21736 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:30:30 (0.031 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:30:30 (0.007 seconds) |
Branch 18
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.245 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 (0.855 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.781 seconds) |
Create merged BAM alignment from unmapped BAM file
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.835 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:46 (26.828 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:46 - 2016-5-16 11:17:9 (22.839 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.654 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:10 (0.549 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.405 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.927 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.006 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.809 seconds) |
| Inputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:15 - 2016-5-16 11:17:17 (1.892 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:17 - 2016-5-16 11:17:44 (26.708 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21427 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:44 - 2016-5-16 11:30:56 (13 minutes, 11.583 seconds) |
| Inputs |
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| Commands | 21745 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:30:56 (0.032 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:30:56 (0.010 seconds) |
Branch 19
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.375 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 (0.978 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (23.168 seconds) |
Create merged BAM alignment from unmapped BAM file
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.186 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:45 (25.584 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:45 - 2016-5-16 11:17:8 (23.525 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.886 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:9 (0.814 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:10 (0.816 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.082 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.148 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:16 (2.016 seconds) |
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| Execution Time | 2016-5-16 11:17:16 - 2016-5-16 11:17:19 (3.346 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:19 - 2016-5-16 11:17:47 (27.661 seconds) |
Collect insert size metrics
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| Commands | 21463 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:47 - 2016-5-16 11:37:0 (19 minutes, 13.539 seconds) |
| Inputs |
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| Commands | 21886 |
| Outputs |
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| Execution Time | 2016-5-16 11:37:0 (0.031 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Execution Time | 2016-5-16 11:37:0 (0.007 seconds) |
Branch 20
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.528 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.270 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.406 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.090 seconds) |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:42 (23.404 seconds) |
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| Execution Time | 2016-5-16 11:16:42 - 2016-5-16 11:17:7 (24.600 seconds) |
Mark Duplicates with PicardTools
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| Execution Time | 2016-5-16 11:17:7 - 2016-5-16 11:17:8 (1.044 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.599 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.834 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:9 (0.995 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:11 (0.990 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:17:12 (0.969 seconds) |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.134 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:40 (26.124 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21403 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:40 - 2016-5-16 11:28:53 (11 minutes, 12.865 seconds) |
| Inputs |
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| Commands | 21699 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:28:53 (0.064 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Execution Time | 2016-5-16 11:28:53 (0.013 seconds) |
Branch 21
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.436 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:54 (0.786 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (22.090 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:17 - 2016-5-16 11:16:19 (1.711 seconds) |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:45 (26.300 seconds) |
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| Execution Time | 2016-5-16 11:16:45 - 2016-5-16 11:17:8 (22.944 seconds) |
Mark Duplicates with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.676 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.709 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.561 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:10 (0.648 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.111 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.036 seconds) |
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| Execution Time | 2016-5-16 11:17:13 (0.874 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:40 (26.241 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21380 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:40 - 2016-5-16 11:26:24 (8 minutes, 43.490 seconds) |
| Inputs |
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| Commands | 21646 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:26:24 (0.035 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Outputs |
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| Execution Time | 2016-5-16 11:26:24 (0.009 seconds) |
Branch 22
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:55 (21.623 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:15:58 (2.680 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:58 - 2016-5-16 11:16:19 (21.079 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:20 (1.158 seconds) |
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| Execution Time | 2016-5-16 11:16:20 - 2016-5-16 11:16:44 (24.114 seconds) |
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| Execution Time | 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (24.231 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.814 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.769 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:10 (0.618 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:11 (0.429 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:13 (1.269 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 (0.835 seconds) |
| Inputs |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.320 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:15 - 2016-5-16 11:17:43 (27.764 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21429 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:43 - 2016-5-16 11:31:45 (14 minutes, 1.990 seconds) |
| Inputs |
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| Commands | 21769 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:31:45 (0.052 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Outputs |
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| Execution Time | 2016-5-16 11:31:45 (0.013 seconds) |
Branch 23
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.787 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:56 (1.905 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:56 - 2016-5-16 11:16:18 (21.837 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.100 seconds) |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (24.413 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:44 - 2016-5-16 11:17:7 (23.556 seconds) |
Mark Duplicates with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:17:7 (0.576 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.629 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.573 seconds) |
Apply BQSR to input BAM file.
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.980 seconds) |
Compare pre and post base-quality scores from recalibration
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.914 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:13 (1.152 seconds) |
| Inputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 (0.873 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:38 (24.287 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21366 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:38 - 2016-5-16 11:23:19 (5 minutes, 41.153 seconds) |
| Inputs |
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| Commands | 21586 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:23:19 (0.041 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Outputs |
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| Execution Time | 2016-5-16 11:23:19 (0.008 seconds) |
Branch 24
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:55 (21.243 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:15:56 (1.216 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:56 - 2016-5-16 11:16:18 (22.098 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 (0.892 seconds) |
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:43 (24.097 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:43 - 2016-5-16 11:17:8 (24.433 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.795 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.913 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.897 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.362 seconds) |
Compare pre and post base-quality scores from recalibration
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.333 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 (0.926 seconds) |
| Inputs |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:16 (2.849 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:16 - 2016-5-16 11:17:41 (25.047 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21431 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:41 - 2016-5-16 11:31:22 (13 minutes, 40.936 seconds) |
| Inputs |
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| Commands | 21757 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:31:22 (0.032 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Outputs |
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| Execution Time | 2016-5-16 11:31:22 (0.012 seconds) |
Branch 25
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Outputs |
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:55 (21.330 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:15:56 (1.518 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:56 - 2016-5-16 11:16:18 (22.160 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:20 (1.350 seconds) |
| Inputs |
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| Execution Time | 2016-5-16 11:16:20 - 2016-5-16 11:16:44 (24.356 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:44 - 2016-5-16 11:17:7 (22.919 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:7 (0.786 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.623 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.669 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:9 (0.871 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:10 (0.868 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:13 (1.261 seconds) |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.333 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:40 (25.998 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21387 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:40 - 2016-5-16 11:25:46 (8 minutes, 6.008 seconds) |
| Inputs |
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| Commands | 21627 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:25:46 (0.041 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Execution Time | 2016-5-16 11:25:46 (0.010 seconds) |
Branch 26
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.054 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.272 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (21.880 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:17 - 2016-5-16 11:16:18 (1.429 seconds) |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:43 (24.657 seconds) |
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| Execution Time | 2016-5-16 11:16:43 - 2016-5-16 11:17:7 (24.016 seconds) |
Mark Duplicates with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:17:7 (0.706 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.664 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.774 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:9 (0.457 seconds) |
Compare pre and post base-quality scores from recalibration
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.842 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.771 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 (0.852 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:34 (21.172 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21341 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:34 - 2016-5-16 11:21:4 (3 minutes, 30.043 seconds) |
| Inputs |
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|---|---|
| Commands | 21526 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:21:4 (0.040 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Outputs |
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| Execution Time | 2016-5-16 11:21:4 (0.008 seconds) |
Branch 27
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.155 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.400 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (21.771 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:17 - 2016-5-16 11:16:18 (1.020 seconds) |
| Inputs |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:42 (24.229 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:43 - 2016-5-16 11:17:7 (24.542 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:7 (0.515 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.783 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:8 (0.930 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.917 seconds) |
Compare pre and post base-quality scores from recalibration
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.793 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:13 (1.234 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 (0.880 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:39 (25.362 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21377 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:39 - 2016-5-16 11:25:33 (7 minutes, 53.805 seconds) |
| Inputs |
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|---|---|
| Commands | 21619 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:25:33 (0.034 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:25:33 (0.009 seconds) |
Branch 28
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.772 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:56 (1.691 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:56 - 2016-5-16 11:16:18 (22.098 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 (0.675 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (24.828 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:44 - 2016-5-16 11:17:7 (23.657 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.792 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.745 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.777 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.757 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.637 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.013 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 (0.992 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:40 (26.418 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21483 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:40 - 2016-5-16 11:37:52 (20 minutes, 11.922 seconds) |
| Inputs |
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|---|---|
| Commands | 21906 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:37:54 (0.038 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:37:54 (0.008 seconds) |
Branch 29
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (21.034 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:56 (1.495 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:56 - 2016-5-16 11:16:18 (22.403 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:20 (1.433 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:20 - 2016-5-16 11:16:47 (26.868 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:47 - 2016-5-16 11:17:10 (22.792 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:10 (0.779 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:11 (0.285 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.917 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 (0.760 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.374 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (2.180 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:16 - 2016-5-16 11:17:18 (2.093 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:19 - 2016-5-16 11:17:46 (27.829 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21458 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:46 - 2016-5-16 11:34:49 (17 minutes, 2.833 seconds) |
| Inputs |
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|---|---|
| Commands | 21841 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:34:49 (0.031 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:34:49 (0.008 seconds) |
Branch 30
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.644 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.336 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (23.132 seconds) |
Create merged BAM alignment from unmapped BAM file
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 (0.774 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (25.159 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.351 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.658 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.590 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.448 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.966 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.463 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.339 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.353 seconds) |
Collect alignment summary statistics
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:40 (25.883 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21386 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:40 - 2016-5-16 11:25:47 (8 minutes, 6.532 seconds) |
| Inputs |
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|---|---|
| Commands | 21631 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:25:47 (0.038 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:25:47 (0.011 seconds) |
Branch 31
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.404 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.292 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.309 seconds) |
Create merged BAM alignment from unmapped BAM file
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.664 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:45 (25.808 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:45 - 2016-5-16 11:17:8 (22.485 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.925 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.557 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.555 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.778 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.190 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.008 seconds) |
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.348 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:15 - 2016-5-16 11:17:40 (25.264 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21374 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:40 - 2016-5-16 11:27:15 (9 minutes, 34.480 seconds) |
| Inputs |
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| Commands | 21658 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:27:15 (0.052 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Outputs |
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| Execution Time | 2016-5-16 11:27:15 (0.011 seconds) |
Branch 32
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:47 (14.466 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:47 (0.088 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:48 - 2016-5-16 11:16:12 (23.916 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:12 - 2016-5-16 11:16:13 (1.932 seconds) |
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| Execution Time | 2016-5-16 11:16:13 - 2016-5-16 11:16:37 (24.005 seconds) |
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| Outputs |
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| Execution Time | 2016-5-16 11:16:38 - 2016-5-16 11:17:3 (25.392 seconds) |
Mark Duplicates with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:17:3 - 2016-5-16 11:17:5 (2.125 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:5 - 2016-5-16 11:17:6 (1.050 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:6 - 2016-5-16 11:17:8 (1.453 seconds) |
Apply BQSR to input BAM file.
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| Tools |
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| Execution Time | 2016-5-16 11:17:8 (0.814 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:8 - 2016-5-16 11:17:10 (1.286 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Execution Time | 2016-5-16 11:17:10 (0.992 seconds) |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.229 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:35 (23.399 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21354 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:36 - 2016-5-16 11:22:27 (4 minutes, 51.087 seconds) |
| Inputs |
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| Commands | 21559 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:22:27 (0.048 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Outputs |
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| Execution Time | 2016-5-16 11:22:27 (0.008 seconds) |
Branch 33
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Outputs |
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.872 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:56 (1.438 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:56 - 2016-5-16 11:16:16 (20.512 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:16 - 2016-5-16 11:16:17 (1.053 seconds) |
| Inputs |
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| Execution Time | 2016-5-16 11:16:17 - 2016-5-16 11:16:39 (21.987 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:39 - 2016-5-16 11:17:5 (25.339 seconds) |
Mark Duplicates with PicardTools
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:5 - 2016-5-16 11:17:7 (2.079 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:7 (0.950 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:8 (0.704 seconds) |
Apply BQSR to input BAM file.
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.808 seconds) |
Compare pre and post base-quality scores from recalibration
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 - 2016-5-16 11:17:11 (1.328 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.958 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.154 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:38 (25.176 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21401 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:38 - 2016-5-16 11:28:47 (11 minutes, 9.081 seconds) |
| Inputs |
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|---|---|
| Commands | 21694 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:28:47 (0.032 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:28:47 (0.007 seconds) |
Branch 34
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:55 (21.695 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:15:57 (1.672 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:57 - 2016-5-16 11:16:19 (22.134 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:21 (1.977 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:21 - 2016-5-16 11:16:47 (25.859 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:47 - 2016-5-16 11:17:9 (21.484 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.822 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:10 (0.315 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.538 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.362 seconds) |
Compare pre and post base-quality scores from recalibration
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:13 (1.489 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.077 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (2.072 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:16 - 2016-5-16 11:17:43 (26.424 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21392 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:43 - 2016-5-16 11:28:5 (10 minutes, 22.114 seconds) |
| Inputs |
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|---|---|
| Commands | 21682 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:28:5 (0.034 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:28:5 (0.008 seconds) |
Branch 35
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.154 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 (0.982 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (22.494 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:17 - 2016-5-16 11:16:19 (1.441 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (25.196 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.884 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.905 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.823 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.727 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.843 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.155 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.090 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (2.232 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:16 - 2016-5-16 11:17:43 (26.830 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21421 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:43 - 2016-5-16 11:30:8 (12 minutes, 24.365 seconds) |
| Inputs |
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|---|---|
| Commands | 21733 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:30:8 (0.043 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:30:8 (0.008 seconds) |
Branch 36
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.088 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.187 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.819 seconds) |
Create merged BAM alignment from unmapped BAM file
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 (0.900 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (25.570 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.802 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.501 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.898 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.795 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.729 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:13 (1.438 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 (0.943 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (2.406 seconds) |
Collect alignment summary statistics
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:16 - 2016-5-16 11:17:45 (28.330 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21466 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:45 - 2016-5-16 11:37:51 (20 minutes, 6.372 seconds) |
| Inputs |
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|---|---|
| Commands | 21901 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:37:51 (0.037 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:37:51 (0.009 seconds) |
Branch 37
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.493 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.023 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (21.685 seconds) |
Create merged BAM alignment from unmapped BAM file
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:17 - 2016-5-16 11:16:19 (1.611 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (25.459 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.657 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.805 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.195 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.702 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 - 2016-5-16 11:17:11 (1.138 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.057 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.084 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.391 seconds) |
Collect alignment summary statistics
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:15 - 2016-5-16 11:17:41 (26.783 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21440 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:41 - 2016-5-16 11:33:11 (15 minutes, 29.113 seconds) |
| Inputs |
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| Commands | 21802 |
| Outputs |
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| Execution Time | 2016-5-16 11:33:11 (0.059 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Execution Time | 2016-5-16 11:33:11 (0.014 seconds) |
Branch 38
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (21.018 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.214 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:56 - 2016-5-16 11:16:18 (22.350 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.375 seconds) |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:46 (26.626 seconds) |
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| Execution Time | 2016-5-16 11:16:46 - 2016-5-16 11:17:9 (22.618 seconds) |
Mark Duplicates with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.780 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.579 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:10 (0.495 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:11 (0.890 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.187 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.106 seconds) |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:17 (2.539 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:17 - 2016-5-16 11:17:42 (25.100 seconds) |
Collect insert size metrics
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| Commands | 21447 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:42 - 2016-5-16 11:33:15 (15 minutes, 33.275 seconds) |
| Inputs |
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| Commands | 21805 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:33:15 (0.032 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Outputs |
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| Execution Time | 2016-5-16 11:33:15 (0.008 seconds) |
Branch 39
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Outputs |
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.524 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.034 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (22.341 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:18 (0.543 seconds) |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:42 (24.374 seconds) |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:42 - 2016-5-16 11:17:7 (24.450 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:17:7 (0.935 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.249 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.383 seconds) |
Apply BQSR to input BAM file.
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.724 seconds) |
Compare pre and post base-quality scores from recalibration
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 - 2016-5-16 11:17:11 (1.247 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.305 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 (0.925 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:37 (24.053 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21358 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:37 - 2016-5-16 11:22:1 (4 minutes, 23.317 seconds) |
| Inputs |
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|---|---|
| Commands | 21550 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:22:1 (0.034 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Outputs |
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| Execution Time | 2016-5-16 11:22:1 (0.008 seconds) |
Branch 40
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.319 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 (0.991 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.431 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:18 (0.746 seconds) |
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:43 (24.154 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:43 - 2016-5-16 11:17:6 (23.147 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:17:6 (0.588 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:6 - 2016-5-16 11:17:8 (1.137 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:8 (0.782 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:8 (0.700 seconds) |
Compare pre and post base-quality scores from recalibration
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.646 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.918 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.882 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:32 (19.863 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21338 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:32 - 2016-5-16 11:18:59 (1 minutes, 27.623 seconds) |
| Inputs |
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|---|---|
| Commands | 21490 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:18:59 (0.032 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:18:59 (0.007 seconds) |
Branch 41
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.935 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 (0.868 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (23.092 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:20 (1.484 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:20 - 2016-5-16 11:16:47 (26.594 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:47 - 2016-5-16 11:17:9 (22.025 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.672 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.649 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.768 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.689 seconds) |
Compare pre and post base-quality scores from recalibration
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 (0.969 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 (0.494 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.554 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:15 - 2016-5-16 11:17:41 (25.856 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21397 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:41 - 2016-5-16 11:27:49 (10 minutes, 7.862 seconds) |
| Inputs |
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| Commands | 21676 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:27:49 (0.036 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:27:49 (0.009 seconds) |
Branch 42
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:48 (14.985 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:48 (0.088 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:48 - 2016-5-16 11:16:12 (23.395 seconds) |
Create merged BAM alignment from unmapped BAM file
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:12 - 2016-5-16 11:16:13 (1.666 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:13 - 2016-5-16 11:16:37 (23.871 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:37 - 2016-5-16 11:17:3 (25.660 seconds) |
Mark Duplicates with PicardTools
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:3 - 2016-5-16 11:17:4 (1.557 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:5 - 2016-5-16 11:17:7 (2.363 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:7 (0.717 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:8 (0.804 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 - 2016-5-16 11:17:10 (1.280 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.808 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.983 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:32 (20.591 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21350 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:32 - 2016-5-16 11:23:8 (5 minutes, 35.860 seconds) |
| Inputs |
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| Commands | 21577 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:23:8 (0.057 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:23:8 (0.014 seconds) |
Branch 43
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (19.610 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 (0.990 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:16 (21.766 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:16 - 2016-5-16 11:16:18 (1.220 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:43 (25.283 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:43 - 2016-5-16 11:17:7 (24.481 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:7 (0.666 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.655 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.579 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.399 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 - 2016-5-16 11:17:11 (1.005 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.054 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.017 seconds) |
Collect alignment summary statistics
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:38 (24.528 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21484 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:38 - 2016-5-16 11:37:53 (20 minutes, 14.596 seconds) |
| Inputs |
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|---|---|
| Commands | 21909 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:37:55 (0.032 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:37:55 (0.008 seconds) |
Branch 44
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:55 (21.311 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:15:57 (2.075 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:57 - 2016-5-16 11:16:18 (20.850 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.080 seconds) |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (24.416 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:44 - 2016-5-16 11:17:7 (23.627 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:7 (0.670 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.704 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.758 seconds) |
Apply BQSR to input BAM file.
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.857 seconds) |
Compare pre and post base-quality scores from recalibration
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.805 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:13 (1.163 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 (0.956 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:38 (23.931 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21378 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:38 - 2016-5-16 11:25:7 (7 minutes, 29.391 seconds) |
| Inputs |
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| Commands | 21610 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:25:7 (0.051 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Outputs |
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| Execution Time | 2016-5-16 11:25:7 (0.012 seconds) |
Branch 45
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:48 (14.436 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:48 (0.056 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:48 - 2016-5-16 11:16:8 (20.480 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:8 - 2016-5-16 11:16:12 (3.403 seconds) |
| Inputs |
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| Execution Time | 2016-5-16 11:16:12 - 2016-5-16 11:16:34 (22.646 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:34 - 2016-5-16 11:17:1 (26.926 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:1 - 2016-5-16 11:17:3 (2.011 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:3 - 2016-5-16 11:17:5 (1.638 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:5 - 2016-5-16 11:17:7 (1.634 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:7 - 2016-5-16 11:17:8 (1.159 seconds) |
Compare pre and post base-quality scores from recalibration
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:8 - 2016-5-16 11:17:9 (1.053 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 - 2016-5-16 11:17:10 (1.193 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.642 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:33 (21.163 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21343 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:33 - 2016-5-16 11:19:51 (2 minutes, 18.504 seconds) |
| Inputs |
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|---|---|
| Commands | 21505 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:19:51 (0.036 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:19:51 (0.014 seconds) |
Branch 46
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:55 (21.230 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:15:56 (1.389 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:56 - 2016-5-16 11:16:18 (22.136 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 (0.864 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:43 (23.513 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:43 - 2016-5-16 11:17:7 (24.149 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:7 (0.575 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.596 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:8 (0.591 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.833 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 - 2016-5-16 11:17:11 (1.010 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.915 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.025 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:36 (22.950 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21383 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:36 - 2016-5-16 11:25:41 (8 minutes, 4.909 seconds) |
| Inputs |
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|---|---|
| Commands | 21622 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:25:41 (0.035 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:25:41 (0.009 seconds) |
Branch 47
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:48 (14.808 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:48 (0.056 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:48 - 2016-5-16 11:16:12 (23.672 seconds) |
Create merged BAM alignment from unmapped BAM file
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:12 (0.698 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:12 - 2016-5-16 11:16:35 (22.495 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:35 - 2016-5-16 11:17:1 (26.450 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:1 - 2016-5-16 11:17:2 (1.093 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:3 - 2016-5-16 11:17:5 (2.400 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:5 - 2016-5-16 11:17:7 (1.810 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:7 (0.749 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:8 (0.938 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.768 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 - 2016-5-16 11:17:11 (1.386 seconds) |
Collect alignment summary statistics
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:28 (17.010 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21339 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:28 - 2016-5-16 11:19:37 (2 minutes, 8.960 seconds) |
| Inputs |
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|---|---|
| Commands | 21499 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:19:37 (0.051 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:19:37 (0.012 seconds) |
Branch 48
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.925 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 (0.970 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.628 seconds) |
Create merged BAM alignment from unmapped BAM file
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.244 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:43 (23.903 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:43 - 2016-5-16 11:17:7 (24.197 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:7 (0.664 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.798 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.811 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.859 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.062 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 (0.812 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 (0.947 seconds) |
Collect alignment summary statistics
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:40 (26.333 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21395 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:40 - 2016-5-16 11:27:56 (10 minutes, 16.052 seconds) |
| Inputs |
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|---|---|
| Commands | 21679 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:27:56 (0.033 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:27:56 (0.008 seconds) |
Branch 49
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.919 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:56 (1.570 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:56 - 2016-5-16 11:16:18 (21.998 seconds) |
Create merged BAM alignment from unmapped BAM file
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:20 (1.458 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:20 - 2016-5-16 11:16:47 (27.303 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:47 - 2016-5-16 11:17:9 (22.230 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.753 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:10 (0.865 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.062 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 (0.868 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.471 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:15 - 2016-5-16 11:17:17 (2.800 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:18 - 2016-5-16 11:17:20 (2.871 seconds) |
Collect alignment summary statistics
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:20 - 2016-5-16 11:17:47 (26.794 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21479 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:47 - 2016-5-16 11:39:0 (21 minutes, 12.644 seconds) |
| Inputs |
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|---|---|
| Commands | 21928 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:39:0 (0.060 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:39:0 (0.012 seconds) |
Branch 50
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.421 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 (0.405 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:16:17 (22.382 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:17 - 2016-5-16 11:16:18 (1.434 seconds) |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:44 (25.777 seconds) |
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| Execution Time | 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.648 seconds) |
Mark Duplicates with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.737 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:8 (0.499 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.737 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:10 (0.780 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.096 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.316 seconds) |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.120 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:41 (26.199 seconds) |
Collect insert size metrics
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| Commands | 21443 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:41 - 2016-5-16 11:33:45 (16 minutes, 4.638 seconds) |
| Inputs |
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| Commands | 21814 |
| Outputs |
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| Execution Time | 2016-5-16 11:33:45 (0.055 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Execution Time | 2016-5-16 11:33:45 (0.007 seconds) |
Branch 51
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:55 (21.090 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:15:57 (1.790 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:57 - 2016-5-16 11:16:20 (23.218 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:20 - 2016-5-16 11:16:22 (2.446 seconds) |
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| Execution Time | 2016-5-16 11:16:22 - 2016-5-16 11:16:49 (26.298 seconds) |
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| Execution Time | 2016-5-16 11:16:49 - 2016-5-16 11:17:10 (21.144 seconds) |
Mark Duplicates with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:17:10 (0.745 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:11 (0.824 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:12 (0.637 seconds) |
Apply BQSR to input BAM file.
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| Outputs |
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| Execution Time | 2016-5-16 11:17:13 (0.815 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (2.015 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Execution Time | 2016-5-16 11:17:16 - 2016-5-16 11:17:19 (3.123 seconds) |
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| Execution Time | 2016-5-16 11:17:19 - 2016-5-16 11:17:21 (2.222 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:21 - 2016-5-16 11:17:47 (26.261 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21481 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:47 - 2016-5-16 11:39:17 (21 minutes, 30.176 seconds) |
| Inputs |
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|---|---|
| Commands | 21931 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:39:17 (0.055 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Outputs |
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| Execution Time | 2016-5-16 11:39:17 (0.012 seconds) |
Branch 52
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:53 (19.236 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Execution Time | 2016-5-16 11:15:53 - 2016-5-16 11:15:55 (1.403 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:16 (21.771 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:16 - 2016-5-16 11:16:18 (1.689 seconds) |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:42 (24.319 seconds) |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:43 - 2016-5-16 11:17:6 (23.838 seconds) |
Mark Duplicates with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:17:6 (0.968 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:7 (0.556 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.842 seconds) |
Apply BQSR to input BAM file.
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.607 seconds) |
Compare pre and post base-quality scores from recalibration
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| Outputs |
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| Execution Time | 2016-5-16 11:17:10 - 2016-5-16 11:17:11 (1.175 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.956 seconds) |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.070 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:38 (24.552 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21390 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:38 - 2016-5-16 11:26:10 (8 minutes, 32.689 seconds) |
| Inputs |
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|---|---|
| Commands | 21640 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:26:10 (0.053 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Outputs |
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| Execution Time | 2016-5-16 11:26:10 (0.013 seconds) |
Branch 53
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Outputs |
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.581 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.418 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.535 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.183 seconds) |
| Inputs |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:45 (25.752 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:45 - 2016-5-16 11:17:8 (23.097 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.816 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.564 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.897 seconds) |
Apply BQSR to input BAM file.
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.017 seconds) |
Compare pre and post base-quality scores from recalibration
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.298 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 (0.761 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:15 (1.590 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:15 - 2016-5-16 11:17:41 (25.573 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21430 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:41 - 2016-5-16 11:31:28 (13 minutes, 46.972 seconds) |
| Inputs |
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|---|---|
| Commands | 21763 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:31:28 (0.038 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:31:28 (0.008 seconds) |
Branch 54
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:47 (14.415 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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|---|---|
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:47 (0.093 seconds) |
Mark Illumina Adapters with PicardTools
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:48 - 2016-5-16 11:16:12 (23.971 seconds) |
Create merged BAM alignment from unmapped BAM file
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:12 (0.878 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:12 - 2016-5-16 11:16:35 (22.247 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:35 - 2016-5-16 11:17:0 (25.135 seconds) |
Mark Duplicates with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:17:0 - 2016-5-16 11:17:1 (1.078 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:1 - 2016-5-16 11:17:2 (1.364 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:2 - 2016-5-16 11:17:4 (1.800 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:4 - 2016-5-16 11:17:6 (2.050 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:6 - 2016-5-16 11:17:7 (1.113 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:7 - 2016-5-16 11:17:9 (1.021 seconds) |
| Inputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 - 2016-5-16 11:17:10 (1.064 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:10 - 2016-5-16 11:17:12 (2.222 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21334 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:18:50 (1 minutes, 38.017 seconds) |
| Inputs |
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|---|---|
| Commands | 21487 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:18:50 (0.035 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:18:50 (0.009 seconds) |
Branch 55
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:55 (20.701 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:15:56 (1.336 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:56 - 2016-5-16 11:16:18 (22.287 seconds) |
Create merged BAM alignment from unmapped BAM file
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:20 (1.650 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:20 - 2016-5-16 11:16:45 (25.377 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:45 - 2016-5-16 11:17:8 (22.470 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.852 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.632 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.400 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.624 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.303 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.121 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.609 seconds) |
Collect alignment summary statistics
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:15 - 2016-5-16 11:17:42 (27.027 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21452 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:42 - 2016-5-16 11:34:18 (16 minutes, 35.941 seconds) |
| Inputs |
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|---|---|
| Commands | 21823 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:34:18 (0.032 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:34:18 (0.008 seconds) |
Branch 56
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.842 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.032 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:20 (24.340 seconds) |
Create merged BAM alignment from unmapped BAM file
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:20 - 2016-5-16 11:16:22 (2.168 seconds) |
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| Execution Time | 2016-5-16 11:16:22 - 2016-5-16 11:16:47 (24.918 seconds) |
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| Execution Time | 2016-5-16 11:16:47 - 2016-5-16 11:17:9 (21.469 seconds) |
Mark Duplicates with PicardTools
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| Execution Time | 2016-5-16 11:17:9 (0.609 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:9 (0.590 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:10 (0.820 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:11 (0.389 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.297 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.714 seconds) |
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| Execution Time | 2016-5-16 11:17:15 - 2016-5-16 11:17:17 (2.487 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:17 - 2016-5-16 11:17:44 (26.640 seconds) |
Collect insert size metrics
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| Commands | 21420 |
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| Execution Time | 2016-5-16 11:17:44 - 2016-5-16 11:30:4 (12 minutes, 20.175 seconds) |
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| Commands | 21724 |
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| Execution Time | 2016-5-16 11:30:4 (0.032 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Execution Time | 2016-5-16 11:30:4 (0.007 seconds) |
Branch 57
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.271 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:54 (0.804 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:16 (21.684 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:17 - 2016-5-16 11:16:18 (1.497 seconds) |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:43 (25.089 seconds) |
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| Execution Time | 2016-5-16 11:16:43 - 2016-5-16 11:17:7 (24.000 seconds) |
Mark Duplicates with PicardTools
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| Execution Time | 2016-5-16 11:17:7 (0.551 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:8 (0.721 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:8 (0.934 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:9 (0.674 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:10 - 2016-5-16 11:17:11 (1.030 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:13 (1.315 seconds) |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.014 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:40 (26.171 seconds) |
Collect insert size metrics
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| Commands | 21385 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:40 - 2016-5-16 11:27:19 (9 minutes, 39.492 seconds) |
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| Commands | 21661 |
| Outputs |
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| Execution Time | 2016-5-16 11:27:19 (0.033 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Execution Time | 2016-5-16 11:27:19 (0.008 seconds) |
Branch 58
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:55 (21.278 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:15:57 (2.389 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:57 - 2016-5-16 11:16:19 (21.893 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:21 (2.191 seconds) |
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| Execution Time | 2016-5-16 11:16:21 - 2016-5-16 11:16:46 (24.877 seconds) |
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| Execution Time | 2016-5-16 11:16:46 - 2016-5-16 11:17:9 (22.536 seconds) |
Mark Duplicates with PicardTools
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| Execution Time | 2016-5-16 11:17:9 (0.636 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:10 (0.788 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:11 (0.713 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:11 (0.934 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:12 (0.938 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.270 seconds) |
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| Execution Time | 2016-5-16 11:17:15 - 2016-5-16 11:17:18 (2.863 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:18 - 2016-5-16 11:17:45 (27.614 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21475 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:45 - 2016-5-16 11:37:33 (19 minutes, 47.999 seconds) |
| Inputs |
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| Commands | 21893 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:37:33 (0.040 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Execution Time | 2016-5-16 11:37:33 (0.011 seconds) |
Branch 59
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.290 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.247 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (22.137 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:17 - 2016-5-16 11:16:19 (1.404 seconds) |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:45 (25.759 seconds) |
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| Execution Time | 2016-5-16 11:16:45 - 2016-5-16 11:17:7 (22.851 seconds) |
Mark Duplicates with PicardTools
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| Execution Time | 2016-5-16 11:17:7 (0.743 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:8 (0.553 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:9 (0.608 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:9 (0.662 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:10 (0.807 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.996 seconds) |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 (0.901 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:39 (26.349 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21446 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:39 - 2016-5-16 11:34:43 (17 minutes, 3.823 seconds) |
| Inputs |
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| Commands | 21838 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:34:43 (0.032 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Outputs |
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| Execution Time | 2016-5-16 11:34:43 (0.007 seconds) |
Branch 60
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:53 (19.559 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:53 - 2016-5-16 11:15:55 (1.477 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:16 (21.905 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:16 - 2016-5-16 11:16:18 (1.345 seconds) |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:40 (22.239 seconds) |
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| Execution Time | 2016-5-16 11:16:40 - 2016-5-16 11:17:5 (24.810 seconds) |
Mark Duplicates with PicardTools
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| Execution Time | 2016-5-16 11:17:5 - 2016-5-16 11:17:7 (1.705 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:7 (0.859 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:8 (0.659 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:8 (0.576 seconds) |
Compare pre and post base-quality scores from recalibration
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.916 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.811 seconds) |
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| Execution Time | 2016-5-16 11:17:11 (0.989 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:35 (23.150 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21349 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:35 - 2016-5-16 11:21:10 (3 minutes, 35.163 seconds) |
| Inputs |
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| Commands | 21529 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:21:10 (0.033 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Outputs |
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| Execution Time | 2016-5-16 11:21:10 (0.008 seconds) |
Branch 61
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.431 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:56 (1.324 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:56 - 2016-5-16 11:16:19 (23.556 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Tools |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:21 (1.165 seconds) |
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| Tools |
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| Execution Time | 2016-5-16 11:16:21 - 2016-5-16 11:16:46 (24.870 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:46 - 2016-5-16 11:17:9 (23.437 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.756 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:10 (0.563 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.722 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.287 seconds) |
Compare pre and post base-quality scores from recalibration
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.224 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.120 seconds) |
| Inputs |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:17 (2.832 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:17 - 2016-5-16 11:17:44 (26.525 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21434 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:44 - 2016-5-16 11:32:34 (14 minutes, 50.320 seconds) |
| Inputs |
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| Commands | 21790 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:32:34 (0.033 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:32:34 (0.008 seconds) |
Branch 62
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.744 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.079 seconds) |
Mark Illumina Adapters with PicardTools
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.905 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:20 (1.362 seconds) |
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| Tools |
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| Execution Time | 2016-5-16 11:16:20 - 2016-5-16 11:16:45 (25.596 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:45 - 2016-5-16 11:17:8 (22.865 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.424 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.672 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:10 (0.846 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:11 (0.347 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.201 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:17:12 (0.931 seconds) |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.068 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:41 (26.567 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21485 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:41 - 2016-5-16 11:37:53 (20 minutes, 12.366 seconds) |
| Inputs |
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| Commands | 21913 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:37:55 (0.033 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Outputs |
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| Execution Time | 2016-5-16 11:37:55 (0.007 seconds) |
Branch 63
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.439 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:56 (1.469 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:56 - 2016-5-16 11:16:19 (22.769 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:20 (1.307 seconds) |
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| Execution Time | 2016-5-16 11:16:20 - 2016-5-16 11:16:45 (24.594 seconds) |
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:16:45 - 2016-5-16 11:17:8 (23.434 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.827 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.553 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.782 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.724 seconds) |
Compare pre and post base-quality scores from recalibration
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.310 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 (0.968 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (1.937 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:16 - 2016-5-16 11:17:42 (26.176 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21455 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:42 - 2016-5-16 11:34:37 (16 minutes, 54.664 seconds) |
| Inputs |
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|---|---|
| Commands | 21832 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:34:37 (0.032 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:34:37 (0.007 seconds) |
Branch 64
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (19.962 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.208 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:16 (21.546 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:16 - 2016-5-16 11:16:18 (1.533 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:42 (24.061 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:42 - 2016-5-16 11:17:7 (25.019 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:7 (0.846 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.840 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.716 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.819 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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|---|---|
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.424 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.889 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 (0.956 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:40 (26.961 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21425 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:40 - 2016-5-16 11:30:49 (13 minutes, 8.897 seconds) |
| Inputs |
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|---|---|
| Commands | 21740 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:30:49 (0.037 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:30:49 (0.008 seconds) |
Branch 65
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.462 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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|---|---|
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 (0.676 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (23.355 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.023 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (25.204 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.397 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.792 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.755 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.706 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.531 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.351 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 (0.736 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 (0.911 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:39 (24.697 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21410 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:39 - 2016-5-16 11:29:51 (12 minutes, 12.419 seconds) |
| Inputs |
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|---|---|
| Commands | 21718 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:29:51 (0.033 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:29:51 (0.008 seconds) |
Branch 66
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.079 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 (0.911 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:16 (21.154 seconds) |
Create merged BAM alignment from unmapped BAM file
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:16 - 2016-5-16 11:16:17 (1.430 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:17 - 2016-5-16 11:16:42 (24.817 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:42 - 2016-5-16 11:17:6 (24.065 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:6 - 2016-5-16 11:17:8 (1.448 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.686 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:8 (0.626 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.821 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.827 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.453 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:13 (1.144 seconds) |
Collect alignment summary statistics
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:36 (23.660 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21381 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:36 - 2016-5-16 11:26:47 (9 minutes, 10.582 seconds) |
| Inputs |
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|---|---|
| Commands | 21649 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:26:47 (0.033 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:26:47 (0.008 seconds) |
Branch 67
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.339 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 (0.776 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.850 seconds) |
Create merged BAM alignment from unmapped BAM file
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.595 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:46 (26.684 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:46 - 2016-5-16 11:17:9 (22.516 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.437 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.349 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.915 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.921 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.230 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.137 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (2.044 seconds) |
Collect alignment summary statistics
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:16 - 2016-5-16 11:17:43 (26.200 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21437 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:43 - 2016-5-16 11:32:29 (14 minutes, 46.529 seconds) |
| Inputs |
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|---|---|
| Commands | 21784 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:32:29 (0.032 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:32:29 (0.008 seconds) |
Branch 68
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.689 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.178 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:16 (21.024 seconds) |
Create merged BAM alignment from unmapped BAM file
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:16 - 2016-5-16 11:16:18 (1.376 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:43 (25.157 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:43 - 2016-5-16 11:17:7 (24.237 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:7 (0.683 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.723 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.674 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.820 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:10 - 2016-5-16 11:17:12 (1.160 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.007 seconds) |
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| Execution Time | 2016-5-16 11:17:13 (0.852 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:41 (27.143 seconds) |
Collect insert size metrics
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| Commands | 21360 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:41 - 2016-5-16 11:22:8 (4 minutes, 26.942 seconds) |
| Inputs |
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| Commands | 21553 |
| Outputs |
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| Execution Time | 2016-5-16 11:22:8 (0.051 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Execution Time | 2016-5-16 11:22:8 (0.008 seconds) |
Branch 69
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.260 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:54 (0.797 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:16 (21.558 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:16 - 2016-5-16 11:16:18 (1.472 seconds) |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:40 (22.106 seconds) |
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| Execution Time | 2016-5-16 11:16:40 - 2016-5-16 11:17:6 (25.535 seconds) |
Mark Duplicates with PicardTools
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| Execution Time | 2016-5-16 11:17:6 - 2016-5-16 11:17:7 (1.434 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:7 (0.757 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.543 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:8 (0.792 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:9 - 2016-5-16 11:17:11 (1.257 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.323 seconds) |
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| Outputs |
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| Execution Time | 2016-5-16 11:17:11 (0.578 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:36 (23.805 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21359 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:36 - 2016-5-16 11:23:7 (5 minutes, 30.850 seconds) |
| Inputs |
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| Commands | 21574 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:23:7 (0.032 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:23:7 (0.008 seconds) |
Branch 70
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:55 (20.606 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:15:56 (1.202 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:56 - 2016-5-16 11:16:18 (22.429 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.136 seconds) |
| Inputs |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:45 (25.894 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:45 - 2016-5-16 11:17:8 (23.131 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.738 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.970 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.752 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.922 seconds) |
Compare pre and post base-quality scores from recalibration
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 (0.926 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 (0.894 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (1.935 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:16 - 2016-5-16 11:17:45 (28.818 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21439 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:45 - 2016-5-16 11:31:49 (14 minutes, 4.233 seconds) |
| Inputs |
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| Commands | 21772 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:31:49 (0.031 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:31:49 (0.008 seconds) |
Branch 71
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.555 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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|---|---|
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 (0.980 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:56 - 2016-5-16 11:16:18 (22.721 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:21 (2.292 seconds) |
| Inputs |
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| Execution Time | 2016-5-16 11:16:21 - 2016-5-16 11:16:45 (24.465 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:45 - 2016-5-16 11:17:8 (23.315 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.715 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.469 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.750 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.943 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.394 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.548 seconds) |
| Inputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:15 - 2016-5-16 11:17:19 (3.762 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:19 - 2016-5-16 11:17:46 (27.846 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21451 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:47 - 2016-5-16 11:34:25 (16 minutes, 38.404 seconds) |
| Inputs |
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|---|---|
| Commands | 21829 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:34:25 (0.035 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:34:25 (0.021 seconds) |
Branch 72
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.568 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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|---|---|
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 (0.993 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.645 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.089 seconds) |
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:43 (24.181 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:43 - 2016-5-16 11:17:7 (24.070 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:7 (0.694 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.849 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.594 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.748 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.705 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 (0.987 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 (0.629 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:38 (25.081 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21352 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:38 - 2016-5-16 11:22:31 (4 minutes, 52.997 seconds) |
| Inputs |
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|---|---|
| Commands | 21562 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:22:31 (0.031 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:22:31 (0.007 seconds) |
Branch 73
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.775 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.439 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:56 - 2016-5-16 11:16:17 (21.009 seconds) |
Create merged BAM alignment from unmapped BAM file
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:17 - 2016-5-16 11:16:19 (2.059 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (25.494 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.710 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.795 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.779 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.927 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.869 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 (0.964 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 (0.990 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (2.496 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:17 - 2016-5-16 11:17:44 (27.600 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21465 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:44 - 2016-5-16 11:36:31 (18 minutes, 46.646 seconds) |
| Inputs |
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|---|---|
| Commands | 21868 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:36:31 (0.033 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:36:31 (0.007 seconds) |
Branch 74
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.749 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:56 (1.334 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:56 - 2016-5-16 11:16:19 (23.390 seconds) |
Create merged BAM alignment from unmapped BAM file
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:22 (2.308 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:22 - 2016-5-16 11:16:47 (25.657 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:48 - 2016-5-16 11:17:10 (22.553 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:10 (0.603 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:11 (0.797 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 (0.787 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 (0.681 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.783 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:15 - 2016-5-16 11:17:18 (2.793 seconds) |
| Inputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:18 - 2016-5-16 11:17:21 (2.804 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:21 - 2016-5-16 11:17:47 (26.266 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21473 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:47 - 2016-5-16 11:38:40 (20 minutes, 52.600 seconds) |
| Inputs |
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| Commands | 21919 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:38:40 (0.054 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Outputs |
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| Execution Time | 2016-5-16 11:38:40 (0.012 seconds) |
Branch 75
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (19.969 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.201 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (22.602 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:17 - 2016-5-16 11:16:19 (1.402 seconds) |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:45 (25.773 seconds) |
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| Outputs |
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| Execution Time | 2016-5-16 11:16:45 - 2016-5-16 11:17:8 (23.024 seconds) |
Mark Duplicates with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.746 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.418 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.759 seconds) |
Apply BQSR to input BAM file.
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 - 2016-5-16 11:17:11 (1.004 seconds) |
Compare pre and post base-quality scores from recalibration
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| Outputs |
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| Execution Time | 2016-5-16 11:17:11 (0.938 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.132 seconds) |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.297 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:41 (26.317 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21412 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:41 - 2016-5-16 11:29:58 (12 minutes, 16.729 seconds) |
| Inputs |
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|---|---|
| Commands | 21721 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:29:58 (0.040 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Outputs |
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| Execution Time | 2016-5-16 11:29:58 (0.010 seconds) |
Branch 76
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Outputs |
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:47 (14.434 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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|---|---|
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:47 (0.089 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:48 - 2016-5-16 11:16:12 (23.954 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Tools |
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| Execution Time | 2016-5-16 11:16:12 (0.087 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:12 - 2016-5-16 11:16:34 (21.948 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:34 - 2016-5-16 11:16:58 (24.184 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:16:58 (0.055 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:16:58 (0.888 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:59 - 2016-5-16 11:17:0 (1.438 seconds) |
Apply BQSR to input BAM file.
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| Outputs |
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| Execution Time | 2016-5-16 11:17:1 - 2016-5-16 11:17:2 (1.357 seconds) |
Compare pre and post base-quality scores from recalibration
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:2 - 2016-5-16 11:17:5 (3.322 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:5 - 2016-5-16 11:17:7 (1.865 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:7 - 2016-5-16 11:17:8 (1.067 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:8 - 2016-5-16 11:17:12 (4.031 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21333 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:19:32 (2 minutes, 19.596 seconds) |
| Inputs |
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|---|---|
| Commands | 21496 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:19:32 (0.033 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:19:32 (0.008 seconds) |
Branch 77
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:53 (19.582 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:53 - 2016-5-16 11:15:55 (1.241 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:16 (21.849 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:16 - 2016-5-16 11:16:18 (1.473 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:43 (24.986 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:43 - 2016-5-16 11:17:7 (24.414 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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|---|---|
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| Outputs |
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| Execution Time | 2016-5-16 11:17:7 (0.634 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.876 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.630 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.751 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.787 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:13 (1.149 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.320 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:39 (25.247 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21369 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:39 - 2016-5-16 11:24:26 (6 minutes, 46.347 seconds) |
| Inputs |
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|---|---|
| Commands | 21593 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:24:26 (0.052 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:24:26 (0.009 seconds) |
Branch 78
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:46 (13.268 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:46 - 2016-5-16 11:15:48 (1.130 seconds) |
Mark Illumina Adapters with PicardTools
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:48 - 2016-5-16 11:16:12 (23.981 seconds) |
Create merged BAM alignment from unmapped BAM file
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:12 - 2016-5-16 11:16:13 (1.450 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:13 - 2016-5-16 11:16:36 (23.267 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:36 - 2016-5-16 11:17:2 (25.943 seconds) |
Mark Duplicates with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:17:2 - 2016-5-16 11:17:5 (2.715 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:5 - 2016-5-16 11:17:6 (1.539 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:7 - 2016-5-16 11:17:8 (1.128 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:8 (0.790 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:8 (0.975 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 - 2016-5-16 11:17:11 (1.125 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.377 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:35 (22.804 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21348 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:35 - 2016-5-16 11:21:48 (4 minutes, 13.332 seconds) |
| Inputs |
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|---|---|
| Commands | 21547 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:21:48 (0.032 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:21:49 (0.007 seconds) |
Branch 79
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (21.152 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:56 (1.911 seconds) |
Mark Illumina Adapters with PicardTools
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:56 - 2016-5-16 11:16:19 (22.406 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:20 (1.567 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:20 - 2016-5-16 11:16:46 (25.641 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:46 - 2016-5-16 11:17:8 (22.392 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.838 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.906 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.807 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 (0.861 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.024 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.128 seconds) |
| Inputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:15 - 2016-5-16 11:17:17 (2.370 seconds) |
Collect alignment summary statistics
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:17 - 2016-5-16 11:17:44 (26.945 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21454 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:44 - 2016-5-16 11:34:4 (16 minutes, 20.167 seconds) |
| Inputs |
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|---|---|
| Commands | 21820 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:34:4 (0.033 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:34:4 (0.008 seconds) |
Branch 80
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.046 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 (0.940 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:16 (21.321 seconds) |
Create merged BAM alignment from unmapped BAM file
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:16 - 2016-5-16 11:16:18 (1.886 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:43 (25.019 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:43 - 2016-5-16 11:17:7 (24.262 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:7 (0.704 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.852 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.666 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.780 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.000 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.022 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 (0.881 seconds) |
Collect alignment summary statistics
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:38 (24.184 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21375 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:38 - 2016-5-16 11:24:49 (7 minutes, 10.963 seconds) |
| Inputs |
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| Commands | 21598 |
| Outputs |
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| Execution Time | 2016-5-16 11:24:49 (0.039 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Execution Time | 2016-5-16 11:24:49 (0.008 seconds) |
Branch 81
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:55 (21.185 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:15:57 (1.916 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:57 - 2016-5-16 11:16:20 (22.774 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:20 - 2016-5-16 11:16:22 (2.282 seconds) |
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| Execution Time | 2016-5-16 11:16:22 - 2016-5-16 11:16:47 (24.794 seconds) |
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| Execution Time | 2016-5-16 11:16:47 - 2016-5-16 11:17:9 (22.207 seconds) |
Mark Duplicates with PicardTools
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| Execution Time | 2016-5-16 11:17:9 (0.675 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:10 (0.939 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:11 (0.711 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:12 (0.910 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.140 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (2.083 seconds) |
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| Execution Time | 2016-5-16 11:17:16 - 2016-5-16 11:17:19 (3.474 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:19 - 2016-5-16 11:17:46 (27.084 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21480 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:46 - 2016-5-16 11:40:19 (22 minutes, 32.710 seconds) |
| Inputs |
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| Commands | 21937 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:40:19 (0.054 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Outputs |
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| Execution Time | 2016-5-16 11:40:19 (0.013 seconds) |
Branch 82
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:49 (15.815 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:49 - 2016-5-16 11:15:51 (1.719 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:51 - 2016-5-16 11:16:12 (20.858 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:12 (0.081 seconds) |
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| Execution Time | 2016-5-16 11:16:12 - 2016-5-16 11:16:35 (23.096 seconds) |
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| Execution Time | 2016-5-16 11:16:35 - 2016-5-16 11:17:1 (26.471 seconds) |
Mark Duplicates with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:17:1 - 2016-5-16 11:17:4 (2.170 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:4 - 2016-5-16 11:17:6 (2.103 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:6 - 2016-5-16 11:17:7 (1.402 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:7 (0.797 seconds) |
Compare pre and post base-quality scores from recalibration
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| Outputs |
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| Execution Time | 2016-5-16 11:17:8 - 2016-5-16 11:17:9 (1.136 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Execution Time | 2016-5-16 11:17:9 - 2016-5-16 11:17:10 (1.148 seconds) |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.492 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:32 (20.713 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21342 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:32 - 2016-5-16 11:20:29 (2 minutes, 57.769 seconds) |
| Inputs |
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| Commands | 21520 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:20:29 (0.053 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Outputs |
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| Execution Time | 2016-5-16 11:20:30 (0.012 seconds) |
Branch 83
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.294 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 (0.972 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.652 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:18 (0.896 seconds) |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:43 (24.547 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:43 - 2016-5-16 11:17:8 (24.329 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.776 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.677 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.678 seconds) |
Apply BQSR to input BAM file.
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| Outputs |
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| Execution Time | 2016-5-16 11:17:10 (0.957 seconds) |
Compare pre and post base-quality scores from recalibration
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.708 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 (0.897 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 (0.393 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:38 (24.427 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21373 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:38 - 2016-5-16 11:25:6 (7 minutes, 28.523 seconds) |
| Inputs |
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|---|---|
| Commands | 21607 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:25:6 (0.035 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Outputs |
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| Execution Time | 2016-5-16 11:25:6 (0.009 seconds) |
Branch 84
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:55 (21.024 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:15:56 (1.175 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:56 - 2016-5-16 11:16:18 (22.235 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:20 (1.946 seconds) |
| Inputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:20 - 2016-5-16 11:16:47 (26.708 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:47 - 2016-5-16 11:17:8 (21.521 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.730 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.714 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.697 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.891 seconds) |
Compare pre and post base-quality scores from recalibration
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.252 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.277 seconds) |
| Inputs |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (2.036 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:16 - 2016-5-16 11:17:43 (26.605 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21448 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:43 - 2016-5-16 11:34:38 (16 minutes, 55.319 seconds) |
| Inputs |
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| Commands | 21835 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:34:38 (0.060 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:34:38 (0.011 seconds) |
Branch 85
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.910 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.129 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (23.171 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:20 (1.278 seconds) |
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:16:20 - 2016-5-16 11:16:46 (26.666 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:47 - 2016-5-16 11:17:9 (22.151 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.702 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:10 (0.854 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.716 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.020 seconds) |
Compare pre and post base-quality scores from recalibration
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 (0.886 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.187 seconds) |
| Inputs |
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| Execution Time | 2016-5-16 11:17:15 - 2016-5-16 11:17:17 (2.357 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:17 - 2016-5-16 11:17:46 (28.826 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21468 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:46 - 2016-5-16 11:36:33 (18 minutes, 47.297 seconds) |
| Inputs |
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| Commands | 21871 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:36:33 (0.035 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:36:33 (0.009 seconds) |
Branch 86
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.574 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.142 seconds) |
Mark Illumina Adapters with PicardTools
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.880 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.073 seconds) |
| Inputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:45 (25.358 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:45 - 2016-5-16 11:17:8 (22.990 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.755 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.514 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.829 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.660 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.104 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.090 seconds) |
| Inputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.490 seconds) |
Collect alignment summary statistics
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:15 - 2016-5-16 11:17:42 (27.032 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21442 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:42 - 2016-5-16 11:33:40 (15 minutes, 57.422 seconds) |
| Inputs |
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| Commands | 21811 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:33:40 (0.034 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:33:40 (0.008 seconds) |
Branch 87
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:55 (20.913 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:15:56 (1.190 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:56 - 2016-5-16 11:16:17 (21.744 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:17 (0.877 seconds) |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:39 (20.917 seconds) |
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| Execution Time | 2016-5-16 11:16:39 - 2016-5-16 11:17:5 (25.992 seconds) |
Mark Duplicates with PicardTools
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| Execution Time | 2016-5-16 11:17:5 - 2016-5-16 11:17:7 (1.312 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:7 (0.537 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:7 (0.735 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:8 (0.860 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:9 - 2016-5-16 11:17:10 (1.159 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:17:10 (0.506 seconds) |
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| Execution Time | 2016-5-16 11:17:11 (0.545 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:32 (20.065 seconds) |
Collect insert size metrics
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| Commands | 21340 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:32 - 2016-5-16 11:18:16 (44.211 seconds) |
| Inputs |
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| Commands | 21402 |
| Outputs |
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| Execution Time | 2016-5-16 11:18:16 (0.096 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Execution Time | 2016-5-16 11:18:16 (0.019 seconds) |
Branch 88
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.774 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:56 (1.438 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:56 - 2016-5-16 11:16:18 (21.613 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:18 (0.987 seconds) |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (25.335 seconds) |
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| Execution Time | 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.668 seconds) |
Mark Duplicates with PicardTools
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| Execution Time | 2016-5-16 11:17:8 (0.763 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:8 (0.758 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:9 (0.596 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:10 (0.715 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.504 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.041 seconds) |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.544 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:15 - 2016-5-16 11:17:40 (25.184 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21404 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:40 - 2016-5-16 11:28:53 (11 minutes, 12.750 seconds) |
| Inputs |
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| Commands | 21698 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:28:53 (0.067 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Outputs |
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| Execution Time | 2016-5-16 11:28:53 (0.013 seconds) |
Branch 89
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.425 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.228 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (23.089 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:20 (1.763 seconds) |
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| Execution Time | 2016-5-16 11:16:20 - 2016-5-16 11:16:46 (25.785 seconds) |
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| Execution Time | 2016-5-16 11:16:46 - 2016-5-16 11:17:8 (22.205 seconds) |
Mark Duplicates with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.873 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.689 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:10 (0.582 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:11 (0.405 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:13 (1.067 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.333 seconds) |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (2.473 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:16 - 2016-5-16 11:17:42 (25.485 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21405 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:42 - 2016-5-16 11:28:11 (10 minutes, 28.956 seconds) |
| Inputs |
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| Commands | 21688 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:28:11 (0.050 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Outputs |
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| Execution Time | 2016-5-16 11:28:11 (0.008 seconds) |
Branch 90
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (21.102 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:56 (1.049 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:56 - 2016-5-16 11:16:19 (23.264 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:21 (2.162 seconds) |
| Inputs |
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| Execution Time | 2016-5-16 11:16:21 - 2016-5-16 11:16:48 (26.584 seconds) |
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| Tools |
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| Execution Time | 2016-5-16 11:16:48 - 2016-5-16 11:17:9 (21.575 seconds) |
Mark Duplicates with PicardTools
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| Execution Time | 2016-5-16 11:17:9 (0.562 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:10 (0.831 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.420 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:11 (0.819 seconds) |
Compare pre and post base-quality scores from recalibration
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 (0.743 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.034 seconds) |
| Inputs |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:17 (2.698 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:17 - 2016-5-16 11:17:45 (28.038 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21467 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:45 - 2016-5-16 11:36:48 (19 minutes, 3.698 seconds) |
| Inputs |
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| Commands | 21882 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:36:48 (0.042 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:36:49 (0.008 seconds) |
Branch 91
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:53 (19.637 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:53 - 2016-5-16 11:15:55 (1.552 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (21.756 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:17 - 2016-5-16 11:16:18 (1.586 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:42 (23.927 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:42 - 2016-5-16 11:17:7 (24.621 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:17:7 (0.398 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.754 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:8 (0.746 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.719 seconds) |
Compare pre and post base-quality scores from recalibration
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.835 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.813 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 (0.911 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:36 (23.091 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21345 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:36 - 2016-5-16 11:19:55 (2 minutes, 19.092 seconds) |
| Inputs |
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| Commands | 21511 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:19:55 (0.032 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:19:55 (0.008 seconds) |
Branch 92
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.425 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 (0.985 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:16 (20.956 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:16 - 2016-5-16 11:16:18 (1.754 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:43 (25.530 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:43 - 2016-5-16 11:17:7 (24.226 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:7 (0.625 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.768 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.754 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.919 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.070 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.117 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.387 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:15 - 2016-5-16 11:17:42 (27.003 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21393 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:42 - 2016-5-16 11:27:11 (9 minutes, 29.463 seconds) |
| Inputs |
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| Commands | 21655 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:27:11 (0.035 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:27:11 (0.008 seconds) |
Branch 93
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:55 (20.984 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:55 (0.875 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:56 - 2016-5-16 11:16:17 (21.811 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:17 - 2016-5-16 11:16:19 (1.388 seconds) |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:45 (26.480 seconds) |
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| Execution Time | 2016-5-16 11:16:45 - 2016-5-16 11:17:8 (22.525 seconds) |
Mark Duplicates with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.697 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.607 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.771 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:10 (0.558 seconds) |
Compare pre and post base-quality scores from recalibration
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.937 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.078 seconds) |
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| Execution Time | 2016-5-16 11:17:13 (0.835 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:39 (25.535 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21372 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:39 - 2016-5-16 11:25:4 (7 minutes, 24.871 seconds) |
| Inputs |
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| Commands | 21604 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:25:4 (0.047 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Execution Time | 2016-5-16 11:25:4 (0.010 seconds) |
Branch 94
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.613 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.145 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:56 - 2016-5-16 11:16:19 (23.603 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:19 (0.977 seconds) |
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| Execution Time | 2016-5-16 11:16:20 - 2016-5-16 11:16:45 (25.341 seconds) |
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:16:46 - 2016-5-16 11:17:8 (22.830 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.650 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.938 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.854 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.928 seconds) |
Compare pre and post base-quality scores from recalibration
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 (0.958 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.317 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:15 - 2016-5-16 11:17:17 (2.442 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:17 - 2016-5-16 11:17:43 (25.720 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21459 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:43 - 2016-5-16 11:36:26 (18 minutes, 42.974 seconds) |
| Inputs |
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|---|---|
| Commands | 21865 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:36:26 (0.032 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:36:26 (0.008 seconds) |
Branch 95
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.251 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.112 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (22.251 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:17 - 2016-5-16 11:16:19 (1.258 seconds) |
| Inputs |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:43 (24.498 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:43 - 2016-5-16 11:17:7 (24.108 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:7 (0.613 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.542 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.681 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.682 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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|---|---|
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.923 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.996 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:14 (1.113 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:39 (25.905 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21407 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:39 - 2016-5-16 11:32:25 (14 minutes, 45.194 seconds) |
| Inputs |
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|---|---|
| Commands | 21781 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:32:25 (0.032 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:32:25 (0.008 seconds) |
Branch 96
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.680 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 (0.927 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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|---|---|
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| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.709 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 (0.816 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:43 (24.100 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:43 - 2016-5-16 11:17:6 (23.337 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:6 - 2016-5-16 11:17:8 (1.213 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.876 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:8 (0.866 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.693 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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|---|---|
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 - 2016-5-16 11:17:11 (1.072 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:13 (1.330 seconds) |
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 (0.857 seconds) |
Collect alignment summary statistics
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:40 (26.951 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21426 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:40 - 2016-5-16 11:31:20 (13 minutes, 39.630 seconds) |
| Inputs |
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|---|---|
| Commands | 21754 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:31:20 (0.052 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:31:20 (0.012 seconds) |
Branch 97
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:47 (14.407 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:47 (0.091 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:48 - 2016-5-16 11:16:8 (20.064 seconds) |
Create merged BAM alignment from unmapped BAM file
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:8 (0.483 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:8 - 2016-5-16 11:16:36 (28.012 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:36 - 2016-5-16 11:16:59 (23.014 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:16:59 - 2016-5-16 11:17:0 (1.143 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:0 - 2016-5-16 11:17:2 (1.441 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:2 - 2016-5-16 11:17:4 (1.618 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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|---|---|
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:4 - 2016-5-16 11:17:6 (1.802 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:6 - 2016-5-16 11:17:8 (2.275 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:8 - 2016-5-16 11:17:9 (1.183 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.885 seconds) |
Collect alignment summary statistics
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:10 - 2016-5-16 11:17:13 (3.095 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21336 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:20:8 (2 minutes, 54.499 seconds) |
| Inputs |
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|---|---|
| Commands | 21514 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:20:8 (0.034 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:20:8 (0.009 seconds) |
Branch 98
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:47 (14.570 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:47 (0.097 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:48 - 2016-5-16 11:16:12 (23.942 seconds) |
Create merged BAM alignment from unmapped BAM file
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:12 (0.080 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:12 - 2016-5-16 11:16:35 (23.042 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:35 - 2016-5-16 11:17:0 (25.498 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:0 - 2016-5-16 11:17:1 (1.134 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:2 - 2016-5-16 11:17:3 (1.145 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:3 - 2016-5-16 11:17:4 (1.067 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:4 - 2016-5-16 11:17:6 (1.836 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:6 - 2016-5-16 11:17:7 (1.352 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:7 (0.983 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:8 (0.986 seconds) |
Collect alignment summary statistics
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 - 2016-5-16 11:17:12 (3.000 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21332 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:19:52 (2 minutes, 40.182 seconds) |
| Inputs |
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|---|---|
| Commands | 21508 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:19:52 (0.055 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:19:52 (0.013 seconds) |
Branch 99
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.325 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 (0.958 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.845 seconds) |
Create merged BAM alignment from unmapped BAM file
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.369 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:45 (25.833 seconds) |
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| Execution Time | 2016-5-16 11:16:45 - 2016-5-16 11:17:8 (23.147 seconds) |
Mark Duplicates with PicardTools
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| Execution Time | 2016-5-16 11:17:8 (0.737 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:9 (0.287 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:10 - 2016-5-16 11:17:11 (1.025 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:11 (0.339 seconds) |
Compare pre and post base-quality scores from recalibration
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| Outputs |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.153 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.195 seconds) |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (2.417 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:16 - 2016-5-16 11:17:43 (27.323 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21418 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:44 - 2016-5-16 11:29:15 (11 minutes, 31.198 seconds) |
| Inputs |
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| Commands | 21712 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:29:15 (0.044 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Execution Time | 2016-5-16 11:29:15 (0.009 seconds) |
Branch 100
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.959 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 (0.906 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (22.018 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:17 - 2016-5-16 11:16:18 (1.321 seconds) |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:41 (22.652 seconds) |
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| Execution Time | 2016-5-16 11:16:41 - 2016-5-16 11:17:7 (25.513 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:17:7 (0.812 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.742 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:8 (0.660 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.904 seconds) |
Compare pre and post base-quality scores from recalibration
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.624 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.574 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.078 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:36 (23.662 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21356 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:36 - 2016-5-16 11:21:12 (3 minutes, 35.986 seconds) |
| Inputs |
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| Commands | 21532 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:21:12 (0.034 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:21:13 (0.009 seconds) |
Branch 101
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Outputs |
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:55 (21.370 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:15:57 (2.732 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:57 - 2016-5-16 11:16:19 (21.780 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:21 (2.304 seconds) |
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| Execution Time | 2016-5-16 11:16:21 - 2016-5-16 11:16:47 (25.300 seconds) |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:47 - 2016-5-16 11:17:9 (22.511 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.530 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:10 (0.623 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.727 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.888 seconds) |
Compare pre and post base-quality scores from recalibration
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 (0.963 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.101 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:17 (2.208 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:17 - 2016-5-16 11:17:43 (26.766 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21409 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:43 - 2016-5-16 11:28:25 (10 minutes, 41.460 seconds) |
| Inputs |
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|---|---|
| Commands | 21691 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:28:25 (0.032 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:28:25 (0.007 seconds) |
Branch 102
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.726 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.137 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (22.101 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:17 - 2016-5-16 11:16:19 (1.517 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (24.964 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.952 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.884 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.653 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.940 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.412 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:13 (1.391 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 (0.984 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:15 (1.191 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:15 - 2016-5-16 11:17:41 (25.772 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21398 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:41 - 2016-5-16 11:27:27 (9 minutes, 46.219 seconds) |
| Inputs |
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|---|---|
| Commands | 21665 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:27:27 (0.042 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:27:27 (0.007 seconds) |
Branch 103
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.382 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.077 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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|---|---|
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| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (23.112 seconds) |
Create merged BAM alignment from unmapped BAM file
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:20 (1.392 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:20 - 2016-5-16 11:16:45 (24.885 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:45 - 2016-5-16 11:17:8 (23.487 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.691 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.749 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.932 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.863 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.030 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 (0.626 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:16 (2.183 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:16 - 2016-5-16 11:17:42 (26.528 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21389 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:42 - 2016-5-16 11:26:11 (8 minutes, 28.368 seconds) |
| Inputs |
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|---|---|
| Commands | 21643 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:26:11 (0.035 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:26:11 (0.008 seconds) |
Branch 104
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:55 (21.077 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:15:56 (1.321 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:56 - 2016-5-16 11:16:19 (23.289 seconds) |
Create merged BAM alignment from unmapped BAM file
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:20 - 2016-5-16 11:16:22 (2.212 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:22 - 2016-5-16 11:16:47 (25.398 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:47 - 2016-5-16 11:17:10 (22.356 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:10 (0.833 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:11 (0.679 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 (0.810 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 (0.660 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 (0.627 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (2.460 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:16 - 2016-5-16 11:17:20 (3.424 seconds) |
Collect alignment summary statistics
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:20 - 2016-5-16 11:17:46 (26.711 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21474 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:46 - 2016-5-16 11:36:39 (18 minutes, 52.854 seconds) |
| Inputs |
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|---|---|
| Commands | 21877 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:36:39 (0.036 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:36:39 (0.008 seconds) |
Branch 105
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.829 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 (0.827 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:16 (21.367 seconds) |
Create merged BAM alignment from unmapped BAM file
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:17 - 2016-5-16 11:16:18 (1.225 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:43 (24.864 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:43 - 2016-5-16 11:17:7 (24.312 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:7 (0.834 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.752 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.679 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:9 (0.774 seconds) |
Compare pre and post base-quality scores from recalibration
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.940 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:13 (1.287 seconds) |
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:17:13 (0.941 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:38 (24.134 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21353 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:38 - 2016-5-16 11:21:19 (3 minutes, 41.294 seconds) |
| Inputs |
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| Commands | 21535 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:21:19 (0.032 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Outputs |
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| Execution Time | 2016-5-16 11:21:19 (0.008 seconds) |
Branch 106
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.615 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:56 (1.348 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:56 - 2016-5-16 11:16:18 (22.437 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:18 (0.581 seconds) |
| Inputs |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (24.992 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (24.379 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.593 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.855 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.589 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.763 seconds) |
Compare pre and post base-quality scores from recalibration
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.102 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.032 seconds) |
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:17 (2.812 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:17 - 2016-5-16 11:17:43 (26.745 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21464 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:43 - 2016-5-16 11:36:3 (18 minutes, 19.907 seconds) |
| Inputs |
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| Commands | 21859 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:36:3 (0.032 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:36:3 (0.007 seconds) |
Branch 107
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (19.770 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.179 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (22.577 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:17 - 2016-5-16 11:16:19 (1.686 seconds) |
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (25.076 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.713 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.670 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.876 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.818 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.790 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:13 (1.350 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 (0.900 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:15 (1.438 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:15 - 2016-5-16 11:17:41 (26.018 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21396 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:41 - 2016-5-16 11:27:27 (9 minutes, 45.931 seconds) |
| Inputs |
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|---|---|
| Commands | 21666 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:27:27 (0.037 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:27:27 (0.008 seconds) |
Branch 108
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.599 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:56 (1.585 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:15:56 - 2016-5-16 11:16:19 (23.156 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Tools |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:21 (1.799 seconds) |
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:16:21 - 2016-5-16 11:16:47 (26.128 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:47 - 2016-5-16 11:17:9 (22.039 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.890 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:10 (0.366 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.106 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 (0.669 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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|---|---|
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 (0.998 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:15 (1.669 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:15 - 2016-5-16 11:17:17 (1.956 seconds) |
Collect alignment summary statistics
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:17:17 - 2016-5-16 11:17:43 (25.997 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21432 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:43 - 2016-5-16 11:31:14 (13 minutes, 30.425 seconds) |
| Inputs |
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|---|---|
| Commands | 21751 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:31:14 (0.031 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:31:14 (0.008 seconds) |
Branch 109
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.354 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.011 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.998 seconds) |
Create merged BAM alignment from unmapped BAM file
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.429 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:43 (23.897 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:43 - 2016-5-16 11:17:8 (24.424 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.625 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.424 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.986 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.887 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.537 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.018 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.481 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:15 - 2016-5-16 11:17:43 (27.750 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21449 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:43 - 2016-5-16 11:34:55 (17 minutes, 11.982 seconds) |
| Inputs |
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|---|---|
| Commands | 21844 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:34:55 (0.033 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:34:55 (0.008 seconds) |
Branch 110
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.398 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:56 (1.592 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:56 - 2016-5-16 11:16:18 (22.007 seconds) |
Create merged BAM alignment from unmapped BAM file
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 (0.802 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (25.367 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:44 - 2016-5-16 11:17:7 (23.216 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:7 (0.688 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.672 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.794 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.511 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.813 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.326 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:14 (1.174 seconds) |
Collect alignment summary statistics
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:40 (26.221 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21399 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:40 - 2016-5-16 11:29:0 (11 minutes, 20.221 seconds) |
| Inputs |
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|---|---|
| Commands | 21703 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:29:0 (0.037 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:29:0 (0.011 seconds) |
Branch 111
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.785 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.079 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.764 seconds) |
Create merged BAM alignment from unmapped BAM file
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 (0.953 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:46 (26.295 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:46 - 2016-5-16 11:17:9 (22.988 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.806 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.920 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.395 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.851 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.029 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:17:13 (0.756 seconds) |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (1.581 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:16 - 2016-5-16 11:17:42 (26.850 seconds) |
Collect insert size metrics
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| Commands | 21445 |
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| Execution Time | 2016-5-16 11:17:42 - 2016-5-16 11:33:8 (15 minutes, 25.481 seconds) |
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| Commands | 21796 |
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| Execution Time | 2016-5-16 11:33:8 (0.035 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Execution Time | 2016-5-16 11:33:8 (0.008 seconds) |
Branch 112
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:48 (15.079 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:48 (0.089 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:48 - 2016-5-16 11:16:8 (19.982 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:8 - 2016-5-16 11:16:12 (3.329 seconds) |
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| Execution Time | 2016-5-16 11:16:12 - 2016-5-16 11:16:33 (21.826 seconds) |
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| Execution Time | 2016-5-16 11:16:33 - 2016-5-16 11:16:58 (24.650 seconds) |
Mark Duplicates with PicardTools
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| Execution Time | 2016-5-16 11:16:58 (0.096 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:16:58 (0.936 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:16:59 - 2016-5-16 11:17:1 (1.475 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:1 - 2016-5-16 11:17:3 (2.054 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:3 - 2016-5-16 11:17:6 (2.955 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:17:6 - 2016-5-16 11:17:8 (1.939 seconds) |
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| Execution Time | 2016-5-16 11:17:8 - 2016-5-16 11:17:9 (1.179 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:9 - 2016-5-16 11:17:12 (3.387 seconds) |
Collect insert size metrics
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| Commands | 21331 |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:19:27 (2 minutes, 14.909 seconds) |
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| Commands | 21493 |
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| Execution Time | 2016-5-16 11:19:27 (0.034 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Execution Time | 2016-5-16 11:19:27 (0.008 seconds) |
Branch 113
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:55 (21.275 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:15:58 (2.652 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:58 - 2016-5-16 11:16:21 (23.525 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:21 - 2016-5-16 11:16:23 (1.505 seconds) |
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| Execution Time | 2016-5-16 11:16:23 - 2016-5-16 11:16:45 (22.689 seconds) |
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| Execution Time | 2016-5-16 11:16:45 - 2016-5-16 11:17:8 (22.420 seconds) |
Mark Duplicates with PicardTools
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| Execution Time | 2016-5-16 11:17:8 (0.688 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:8 (0.653 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:9 (0.819 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:10 (0.686 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.633 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.001 seconds) |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:15 (1.750 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:15 - 2016-5-16 11:17:43 (27.920 seconds) |
Collect insert size metrics
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| Commands | 21400 |
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| Execution Time | 2016-5-16 11:17:43 - 2016-5-16 11:29:10 (11 minutes, 26.365 seconds) |
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| Commands | 21709 |
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| Execution Time | 2016-5-16 11:29:10 (0.035 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Execution Time | 2016-5-16 11:29:10 (0.007 seconds) |
Branch 114
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.296 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:54 (0.754 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (22.267 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:17 (0.869 seconds) |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:44 (26.356 seconds) |
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| Execution Time | 2016-5-16 11:16:44 - 2016-5-16 11:17:9 (24.456 seconds) |
Mark Duplicates with PicardTools
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| Execution Time | 2016-5-16 11:17:9 (0.715 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:9 (0.468 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:10 (0.541 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.062 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.133 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:17:13 (0.784 seconds) |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:17 (3.017 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:17 - 2016-5-16 11:17:45 (27.610 seconds) |
Collect insert size metrics
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| Commands | 21472 |
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| Execution Time | 2016-5-16 11:17:45 - 2016-5-16 11:37:8 (19 minutes, 23.608 seconds) |
| Inputs |
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| Commands | 21889 |
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| Execution Time | 2016-5-16 11:37:8 (0.033 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Execution Time | 2016-5-16 11:37:8 (0.008 seconds) |
Branch 115
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:55 (21.210 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:15:57 (2.547 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:57 - 2016-5-16 11:16:19 (21.990 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:21 (1.924 seconds) |
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| Execution Time | 2016-5-16 11:16:21 - 2016-5-16 11:16:46 (24.533 seconds) |
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| Execution Time | 2016-5-16 11:16:46 - 2016-5-16 11:17:9 (23.442 seconds) |
Mark Duplicates with PicardTools
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| Execution Time | 2016-5-16 11:17:9 (0.613 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:10 (0.773 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:11 (0.626 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:12 (0.934 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.240 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (1.931 seconds) |
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| Execution Time | 2016-5-16 11:17:16 - 2016-5-16 11:17:20 (3.736 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:20 - 2016-5-16 11:17:46 (26.867 seconds) |
Collect insert size metrics
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| Commands | 21478 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:46 - 2016-5-16 11:38:12 (20 minutes, 25.894 seconds) |
| Inputs |
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| Commands | 21916 |
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| Execution Time | 2016-5-16 11:38:12 (0.067 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Execution Time | 2016-5-16 11:38:12 (0.014 seconds) |
Branch 116
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.974 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.203 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.470 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:18 (0.802 seconds) |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:45 (26.253 seconds) |
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| Execution Time | 2016-5-16 11:16:45 - 2016-5-16 11:17:8 (23.275 seconds) |
Mark Duplicates with PicardTools
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| Execution Time | 2016-5-16 11:17:8 (0.700 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:9 (0.691 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:10 (0.818 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:11 (0.666 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.446 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.713 seconds) |
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| Execution Time | 2016-5-16 11:17:15 - 2016-5-16 11:17:16 (1.547 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:17 - 2016-5-16 11:17:46 (29.730 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21470 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:46 - 2016-5-16 11:37:40 (19 minutes, 53.439 seconds) |
| Inputs |
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| Commands | 21898 |
| Outputs |
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| Execution Time | 2016-5-16 11:37:40 (0.054 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Execution Time | 2016-5-16 11:37:40 (0.011 seconds) |
Branch 117
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.360 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:54 (0.821 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (22.216 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:17 - 2016-5-16 11:16:18 (1.169 seconds) |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:40 (22.010 seconds) |
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| Execution Time | 2016-5-16 11:16:40 - 2016-5-16 11:17:5 (24.781 seconds) |
Mark Duplicates with PicardTools
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| Execution Time | 2016-5-16 11:17:5 - 2016-5-16 11:17:7 (2.271 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:7 (0.601 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:8 (0.764 seconds) |
Apply BQSR to input BAM file.
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.771 seconds) |
Compare pre and post base-quality scores from recalibration
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.994 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.006 seconds) |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.064 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:38 (25.122 seconds) |
Collect insert size metrics
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| Commands | 21371 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:38 - 2016-5-16 11:25:19 (7 minutes, 40.791 seconds) |
| Inputs |
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| Commands | 21616 |
| Outputs |
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| Execution Time | 2016-5-16 11:25:19 (0.035 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Execution Time | 2016-5-16 11:25:19 (0.009 seconds) |
Branch 118
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:48 (15.378 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:48 - 2016-5-16 11:15:51 (2.858 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:51 - 2016-5-16 11:16:13 (21.523 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:13 (0.781 seconds) |
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| Execution Time | 2016-5-16 11:16:14 - 2016-5-16 11:16:36 (22.681 seconds) |
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| Execution Time | 2016-5-16 11:16:36 - 2016-5-16 11:17:3 (26.385 seconds) |
Mark Duplicates with PicardTools
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| Execution Time | 2016-5-16 11:17:3 - 2016-5-16 11:17:4 (1.559 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:4 - 2016-5-16 11:17:6 (2.043 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:6 (0.804 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:7 (0.747 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:8 - 2016-5-16 11:17:9 (1.262 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:17:9 - 2016-5-16 11:17:11 (1.364 seconds) |
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| Execution Time | 2016-5-16 11:17:11 (0.977 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:32 (20.262 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21344 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:32 - 2016-5-16 11:20:53 (3 minutes, 21.045 seconds) |
| Inputs |
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| Commands | 21523 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:20:53 (0.033 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Outputs |
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| Execution Time | 2016-5-16 11:20:53 (0.007 seconds) |
Branch 119
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.321 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.019 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (23.331 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:20 (1.534 seconds) |
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| Execution Time | 2016-5-16 11:16:20 - 2016-5-16 11:16:45 (25.514 seconds) |
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| Outputs |
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| Execution Time | 2016-5-16 11:16:45 - 2016-5-16 11:17:9 (23.307 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.832 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:10 (0.751 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.684 seconds) |
Apply BQSR to input BAM file.
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.966 seconds) |
Compare pre and post base-quality scores from recalibration
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| Outputs |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.056 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:15 (1.878 seconds) |
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| Execution Time | 2016-5-16 11:17:15 - 2016-5-16 11:17:18 (2.260 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:18 - 2016-5-16 11:17:46 (28.684 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21477 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:46 - 2016-5-16 11:38:56 (21 minutes, 9.438 seconds) |
| Inputs |
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| Commands | 21923 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:38:56 (0.051 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Outputs |
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| Execution Time | 2016-5-16 11:38:56 (0.011 seconds) |
Branch 120
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.152 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 (0.917 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (22.294 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:17 - 2016-5-16 11:16:18 (1.176 seconds) |
| Inputs |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:43 (25.116 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:43 - 2016-5-16 11:17:7 (23.552 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:17:7 (0.519 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.605 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.581 seconds) |
Apply BQSR to input BAM file.
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.780 seconds) |
Compare pre and post base-quality scores from recalibration
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 - 2016-5-16 11:17:11 (1.210 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:13 (1.516 seconds) |
| Inputs |
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| Execution Time | 2016-5-16 11:17:13 (0.940 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:39 (25.700 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21406 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:39 - 2016-5-16 11:28:10 (10 minutes, 30.506 seconds) |
| Inputs |
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|---|---|
| Commands | 21685 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:28:10 (0.033 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:28:10 (0.008 seconds) |
Branch 121
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (19.780 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 (0.980 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:16 (21.599 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Outputs |
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| Execution Time | 2016-5-16 11:16:16 - 2016-5-16 11:16:18 (1.440 seconds) |
| Inputs |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:40 (22.130 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:40 - 2016-5-16 11:17:3 (23.530 seconds) |
Mark Duplicates with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:17:4 - 2016-5-16 11:17:5 (1.420 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:5 (0.974 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:6 - 2016-5-16 11:17:7 (1.086 seconds) |
Apply BQSR to input BAM file.
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:7 (0.729 seconds) |
Compare pre and post base-quality scores from recalibration
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:8 - 2016-5-16 11:17:9 (1.079 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 - 2016-5-16 11:17:11 (1.379 seconds) |
| Inputs |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.241 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:34 (21.622 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21355 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:34 - 2016-5-16 11:22:48 (5 minutes, 13.936 seconds) |
| Inputs |
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|---|---|
| Commands | 21568 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:22:48 (0.034 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:22:48 (0.009 seconds) |
Branch 122
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.668 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.166 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.122 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 (0.974 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:43 (24.522 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:43 - 2016-5-16 11:17:8 (24.267 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.505 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.469 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.718 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.330 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.936 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.890 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.063 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:39 (25.579 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21347 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:39 - 2016-5-16 11:21:25 (3 minutes, 46.090 seconds) |
| Inputs |
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| Commands | 21541 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:21:25 (0.036 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:21:25 (0.008 seconds) |
Branch 123
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.503 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.085 seconds) |
Mark Illumina Adapters with PicardTools
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.868 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.440 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:47 (27.753 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:47 - 2016-5-16 11:17:9 (22.030 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.736 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:10 (0.628 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.401 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:13 (1.034 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 (0.999 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (2.118 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:16 - 2016-5-16 11:17:18 (2.117 seconds) |
Collect alignment summary statistics
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:18 - 2016-5-16 11:17:44 (25.652 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21441 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:44 - 2016-5-16 11:33:57 (16 minutes, 13.741 seconds) |
| Inputs |
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| Commands | 21817 |
| Outputs |
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| Execution Time | 2016-5-16 11:33:57 (0.031 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Execution Time | 2016-5-16 11:33:57 (0.008 seconds) |
Branch 124
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.025 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.138 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (21.569 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:17 - 2016-5-16 11:16:18 (1.255 seconds) |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:40 (22.066 seconds) |
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| Execution Time | 2016-5-16 11:16:40 - 2016-5-16 11:17:7 (26.871 seconds) |
Mark Duplicates with PicardTools
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| Execution Time | 2016-5-16 11:17:7 (0.848 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:8 (0.697 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:9 (0.700 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:9 (0.570 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:10 (0.860 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.046 seconds) |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.034 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:38 (24.648 seconds) |
Collect insert size metrics
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| Commands | 21362 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:38 - 2016-5-16 11:23:15 (5 minutes, 37.407 seconds) |
| Inputs |
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| Commands | 21583 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:23:15 (0.035 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Execution Time | 2016-5-16 11:23:15 (0.007 seconds) |
Branch 125
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:55 (21.149 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:15:56 (1.854 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:57 - 2016-5-16 11:16:21 (23.977 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:21 - 2016-5-16 11:16:22 (1.728 seconds) |
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| Execution Time | 2016-5-16 11:16:22 - 2016-5-16 11:16:48 (25.439 seconds) |
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| Execution Time | 2016-5-16 11:16:48 - 2016-5-16 11:17:10 (22.361 seconds) |
Mark Duplicates with PicardTools
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| Execution Time | 2016-5-16 11:17:10 (0.364 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:11 (0.331 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.024 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:13 (0.865 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.292 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:17:15 - 2016-5-16 11:17:17 (2.522 seconds) |
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| Execution Time | 2016-5-16 11:17:17 - 2016-5-16 11:17:20 (3.216 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:21 - 2016-5-16 11:17:47 (26.130 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21471 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:47 - 2016-5-16 11:38:56 (21 minutes, 9.241 seconds) |
| Inputs |
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| Commands | 21924 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:38:56 (0.039 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Outputs |
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| Execution Time | 2016-5-16 11:38:56 (0.010 seconds) |
Branch 126
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.686 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.110 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (23.445 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:21 (2.154 seconds) |
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| Execution Time | 2016-5-16 11:16:21 - 2016-5-16 11:16:44 (22.965 seconds) |
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| Execution Time | 2016-5-16 11:16:44 - 2016-5-16 11:17:7 (23.295 seconds) |
Mark Duplicates with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:17:7 (0.942 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.541 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.802 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:9 (0.763 seconds) |
Compare pre and post base-quality scores from recalibration
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.523 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.173 seconds) |
| Inputs |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.027 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:39 (26.049 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21379 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:39 - 2016-5-16 11:25:18 (7 minutes, 38.922 seconds) |
| Inputs |
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| Commands | 21613 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:25:18 (0.057 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Outputs |
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| Execution Time | 2016-5-16 11:25:18 (0.013 seconds) |
Branch 127
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Outputs |
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (21.171 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 (0.717 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.589 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.107 seconds) |
| Inputs |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (24.688 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.991 seconds) |
Mark Duplicates with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.484 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.825 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.582 seconds) |
Apply BQSR to input BAM file.
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.779 seconds) |
Compare pre and post base-quality scores from recalibration
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.802 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.075 seconds) |
| Inputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 (0.905 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:41 (27.491 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21414 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:41 - 2016-5-16 11:29:31 (11 minutes, 49.570 seconds) |
| Inputs |
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| Commands | 21715 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:29:31 (0.043 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:29:31 (0.009 seconds) |
Branch 128
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:55 (20.905 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:15:56 (1.163 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:56 - 2016-5-16 11:16:19 (22.890 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:20 (1.055 seconds) |
| Inputs |
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| Execution Time | 2016-5-16 11:16:20 - 2016-5-16 11:16:44 (24.247 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.147 seconds) |
Mark Duplicates with PicardTools
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.817 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.638 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.732 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.696 seconds) |
Compare pre and post base-quality scores from recalibration
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.077 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 (0.922 seconds) |
| Inputs |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.307 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:42 (27.546 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21433 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:42 - 2016-5-16 11:33:9 (15 minutes, 27.662 seconds) |
| Inputs |
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| Commands | 21799 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:33:9 (0.036 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:33:9 (0.012 seconds) |
Branch 129
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.428 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.197 seconds) |
Mark Illumina Adapters with PicardTools
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:20 (24.074 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:20 - 2016-5-16 11:16:23 (2.952 seconds) |
| Inputs |
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| Execution Time | 2016-5-16 11:16:23 - 2016-5-16 11:16:49 (26.606 seconds) |
| Inputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:49 - 2016-5-16 11:17:9 (19.689 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.762 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:10 (0.644 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.428 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.814 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.154 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.228 seconds) |
| Inputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:17 (2.861 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:17 - 2016-5-16 11:17:45 (27.549 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21482 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:45 - 2016-5-16 11:40:5 (22 minutes, 20.108 seconds) |
| Inputs |
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| Commands | 21934 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:40:5 (0.033 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:40:5 (0.008 seconds) |
Branch 130
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.802 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:56 (1.720 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:56 - 2016-5-16 11:16:18 (22.386 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:20 (1.480 seconds) |
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| Execution Time | 2016-5-16 11:16:20 - 2016-5-16 11:16:46 (26.082 seconds) |
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| Execution Time | 2016-5-16 11:16:46 - 2016-5-16 11:17:9 (23.254 seconds) |
Mark Duplicates with PicardTools
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| Execution Time | 2016-5-16 11:17:9 (0.677 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:10 (0.666 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:11 (0.323 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:11 (0.888 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:12 (0.980 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.483 seconds) |
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| Execution Time | 2016-5-16 11:17:15 - 2016-5-16 11:17:17 (2.252 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:17 - 2016-5-16 11:17:45 (27.607 seconds) |
Collect insert size metrics
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| Commands | 21438 |
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| Execution Time | 2016-5-16 11:17:45 - 2016-5-16 11:32:4 (14 minutes, 18.877 seconds) |
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| Commands | 21778 |
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| Execution Time | 2016-5-16 11:32:4 (0.037 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Execution Time | 2016-5-16 11:32:4 (0.009 seconds) |
Branch 131
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:55 (21.208 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:15:57 (2.098 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:57 - 2016-5-16 11:16:19 (22.108 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:21 (2.358 seconds) |
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| Execution Time | 2016-5-16 11:16:22 - 2016-5-16 11:16:49 (27.450 seconds) |
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| Execution Time | 2016-5-16 11:16:49 - 2016-5-16 11:17:8 (19.491 seconds) |
Mark Duplicates with PicardTools
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| Execution Time | 2016-5-16 11:17:9 (0.808 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:9 (0.221 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:10 (0.838 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.051 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.322 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.285 seconds) |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (1.564 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:16 - 2016-5-16 11:17:42 (25.795 seconds) |
Collect insert size metrics
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| Commands | 21450 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:42 - 2016-5-16 11:35:39 (17 minutes, 57.118 seconds) |
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| Commands | 21855 |
| Outputs |
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| Execution Time | 2016-5-16 11:35:39 (0.046 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Execution Time | 2016-5-16 11:35:39 (0.012 seconds) |
Branch 132
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.721 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.268 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.684 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.100 seconds) |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:45 (25.725 seconds) |
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| Execution Time | 2016-5-16 11:16:45 - 2016-5-16 11:17:8 (23.520 seconds) |
Mark Duplicates with PicardTools
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| Execution Time | 2016-5-16 11:17:8 (0.697 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:9 - 2016-5-16 11:17:10 (1.028 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:10 (0.345 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.067 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:12 (0.907 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.190 seconds) |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (1.491 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:16 - 2016-5-16 11:17:42 (25.938 seconds) |
Collect insert size metrics
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| Commands | 21424 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:42 - 2016-5-16 11:31:58 (14 minutes, 16.294 seconds) |
| Inputs |
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| Commands | 21775 |
| Outputs |
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| Execution Time | 2016-5-16 11:31:58 (0.031 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Execution Time | 2016-5-16 11:31:58 (0.007 seconds) |
Branch 133
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.635 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.030 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.231 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:18 (0.966 seconds) |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:43 (24.048 seconds) |
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| Execution Time | 2016-5-16 11:16:43 - 2016-5-16 11:17:7 (24.557 seconds) |
Mark Duplicates with PicardTools
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| Execution Time | 2016-5-16 11:17:7 (0.576 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:8 (0.864 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:9 (0.763 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:10 (0.995 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.273 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:17:12 (0.906 seconds) |
| Inputs |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.359 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:15 - 2016-5-16 11:17:40 (25.836 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21370 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:40 - 2016-5-16 11:24:58 (7 minutes, 17.760 seconds) |
| Inputs |
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| Commands | 21601 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:24:58 (0.034 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Execution Time | 2016-5-16 11:24:58 (0.012 seconds) |
Branch 134
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:55 (21.158 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:15:57 (2.752 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:57 - 2016-5-16 11:16:20 (22.718 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:20 - 2016-5-16 11:16:22 (2.127 seconds) |
| Inputs |
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| Execution Time | 2016-5-16 11:16:22 - 2016-5-16 11:16:49 (26.633 seconds) |
| Inputs |
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| Execution Time | 2016-5-16 11:16:49 - 2016-5-16 11:17:10 (20.929 seconds) |
Mark Duplicates with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:17:10 (0.572 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:11 (0.253 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.000 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:12 (0.661 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.158 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (2.126 seconds) |
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| Execution Time | 2016-5-16 11:17:16 - 2016-5-16 11:17:20 (3.135 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:20 - 2016-5-16 11:17:46 (25.971 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21476 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:46 - 2016-5-16 11:37:33 (19 minutes, 47.820 seconds) |
| Inputs |
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| Commands | 21894 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:37:33 (0.041 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Outputs |
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| Execution Time | 2016-5-16 11:37:33 (0.010 seconds) |
Branch 135
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:53 (19.628 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Execution Time | 2016-5-16 11:15:53 - 2016-5-16 11:15:55 (1.459 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.781 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.219 seconds) |
| Inputs |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (24.966 seconds) |
| Inputs |
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| Execution Time | 2016-5-16 11:16:44 - 2016-5-16 11:17:7 (23.035 seconds) |
Mark Duplicates with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:17:7 (0.874 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.719 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.722 seconds) |
Apply BQSR to input BAM file.
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.468 seconds) |
Compare pre and post base-quality scores from recalibration
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 - 2016-5-16 11:17:11 (1.028 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.910 seconds) |
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:17:12 (0.836 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:37 (23.912 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21363 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:37 - 2016-5-16 11:22:37 (4 minutes, 59.726 seconds) |
| Inputs |
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| Commands | 21565 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:22:37 (0.033 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Outputs |
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| Execution Time | 2016-5-16 11:22:37 (0.009 seconds) |
Branch 136
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.292 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Execution Time | 2016-5-16 11:15:54 (0.866 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:17 (21.658 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:17 - 2016-5-16 11:16:18 (1.118 seconds) |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:42 (24.360 seconds) |
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| Execution Time | 2016-5-16 11:16:42 - 2016-5-16 11:17:7 (24.708 seconds) |
Mark Duplicates with PicardTools
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| Execution Time | 2016-5-16 11:17:7 (0.662 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:8 (0.680 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:8 (0.630 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:9 (0.783 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:10 (0.910 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:17:11 (0.855 seconds) |
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| Execution Time | 2016-5-16 11:17:12 (0.906 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:38 (25.302 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21361 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:38 - 2016-5-16 11:22:25 (4 minutes, 46.653 seconds) |
| Inputs |
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| Commands | 21556 |
| Outputs |
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| Execution Time | 2016-5-16 11:22:25 (0.034 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Execution Time | 2016-5-16 11:22:25 (0.008 seconds) |
Branch 137
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.785 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:54 (0.731 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.522 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.535 seconds) |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:42 (22.845 seconds) |
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| Execution Time | 2016-5-16 11:16:42 - 2016-5-16 11:17:7 (25.187 seconds) |
Mark Duplicates with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:17:7 (0.612 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.553 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.680 seconds) |
Apply BQSR to input BAM file.
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| Outputs |
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| Execution Time | 2016-5-16 11:17:9 - 2016-5-16 11:17:11 (1.061 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:11 (0.689 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.049 seconds) |
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| Outputs |
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| Execution Time | 2016-5-16 11:17:13 (0.757 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:38 (24.853 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21416 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:38 - 2016-5-16 11:29:2 (11 minutes, 23.969 seconds) |
| Inputs |
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| Commands | 21706 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:29:2 (0.034 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Execution Time | 2016-5-16 11:29:2 (0.008 seconds) |
Branch 138
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.389 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.277 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.726 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:18 (0.721 seconds) |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (25.236 seconds) |
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| Execution Time | 2016-5-16 11:16:44 - 2016-5-16 11:17:7 (23.205 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:17:7 (0.525 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.759 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:8 (0.882 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.629 seconds) |
Compare pre and post base-quality scores from recalibration
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.909 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.002 seconds) |
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| Execution Time | 2016-5-16 11:17:12 (0.823 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:40 (26.563 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21376 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:40 - 2016-5-16 11:25:46 (8 minutes, 6.247 seconds) |
| Inputs |
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| Commands | 21626 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:25:46 (0.038 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:25:46 (0.012 seconds) |
Branch 139
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.623 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:56 (1.494 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:56 - 2016-5-16 11:16:18 (22.451 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:20 (1.356 seconds) |
| Inputs |
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| Execution Time | 2016-5-16 11:16:20 - 2016-5-16 11:16:44 (23.868 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (24.719 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.446 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.600 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.648 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.858 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.890 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.022 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 (0.783 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:41 (27.316 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21423 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:41 - 2016-5-16 11:30:49 (13 minutes, 7.799 seconds) |
| Inputs |
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|---|---|
| Commands | 21741 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:30:49 (0.035 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:30:49 (0.008 seconds) |
Branch 140
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:55 (21.155 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:55 (0.835 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.927 seconds) |
Create merged BAM alignment from unmapped BAM file
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:20 (1.475 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:20 - 2016-5-16 11:16:44 (24.317 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.404 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.644 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.709 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.712 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.579 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.767 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.882 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 (0.826 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:39 (25.458 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21391 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:39 - 2016-5-16 11:27:44 (10 minutes, 5.721 seconds) |
| Inputs |
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|---|---|
| Commands | 21673 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:27:44 (0.034 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:27:44 (0.008 seconds) |
Branch 141
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:55 (20.885 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:15:56 (1.791 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:57 - 2016-5-16 11:16:18 (21.874 seconds) |
Create merged BAM alignment from unmapped BAM file
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:20 (1.894 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:20 - 2016-5-16 11:16:46 (25.692 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:46 - 2016-5-16 11:17:9 (22.450 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.660 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.296 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.902 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.875 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.325 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.094 seconds) |
| Inputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:17 (2.809 seconds) |
Collect alignment summary statistics
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:17 - 2016-5-16 11:17:44 (27.137 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21460 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:44 - 2016-5-16 11:36:34 (18 minutes, 49.483 seconds) |
| Inputs |
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| Commands | 21874 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:36:34 (0.047 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:36:34 (0.008 seconds) |
Branch 142
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.229 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.258 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.752 seconds) |
Create merged BAM alignment from unmapped BAM file
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.443 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:20 - 2016-5-16 11:16:45 (25.427 seconds) |
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| Execution Time | 2016-5-16 11:16:45 - 2016-5-16 11:17:8 (22.984 seconds) |
Mark Duplicates with PicardTools
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| Execution Time | 2016-5-16 11:17:8 (0.778 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:9 (0.688 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:10 (0.993 seconds) |
Apply BQSR to input BAM file.
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| Execution Time | 2016-5-16 11:17:11 (0.722 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.489 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.352 seconds) |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:17 (2.356 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:17 - 2016-5-16 11:17:44 (27.446 seconds) |
Collect insert size metrics
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| Commands | 21457 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:44 - 2016-5-16 11:35:0 (17 minutes, 15.681 seconds) |
| Inputs |
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| Commands | 21847 |
| Outputs |
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| Execution Time | 2016-5-16 11:35:0 (0.035 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Execution Time | 2016-5-16 11:35:0 (0.011 seconds) |
Branch 143
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.857 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:54 (0.825 seconds) |
Mark Illumina Adapters with PicardTools
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.734 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.408 seconds) |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:47 (27.886 seconds) |
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| Execution Time | 2016-5-16 11:16:47 - 2016-5-16 11:17:9 (22.297 seconds) |
Mark Duplicates with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.758 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:10 (0.658 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:11 (0.853 seconds) |
Apply BQSR to input BAM file.
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 (0.736 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:13 (0.881 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (2.143 seconds) |
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| Execution Time | 2016-5-16 11:17:16 - 2016-5-16 11:17:19 (3.306 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:19 - 2016-5-16 11:17:46 (26.521 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21435 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:46 - 2016-5-16 11:33:18 (15 minutes, 32.290 seconds) |
| Inputs |
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| Commands | 21808 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:33:18 (0.033 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Execution Time | 2016-5-16 11:33:18 (0.007 seconds) |
Branch 144
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.552 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.147 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.899 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:21 (2.377 seconds) |
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| Execution Time | 2016-5-16 11:16:21 - 2016-5-16 11:16:44 (23.153 seconds) |
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| Execution Time | 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.978 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.788 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.679 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.822 seconds) |
Apply BQSR to input BAM file.
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.386 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.219 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 (0.996 seconds) |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.499 seconds) |
Collect alignment summary statistics
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| Execution Time | 2016-5-16 11:17:15 - 2016-5-16 11:17:40 (24.659 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21368 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:40 - 2016-5-16 11:24:26 (6 minutes, 45.950 seconds) |
| Inputs |
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| Commands | 21594 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:24:26 (0.035 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Outputs |
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| Execution Time | 2016-5-16 11:24:26 (0.011 seconds) |
Branch 145
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.060 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 (0.980 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.847 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:18 (0.950 seconds) |
| Inputs |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:43 (24.928 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (24.484 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.710 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.637 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.784 seconds) |
Apply BQSR to input BAM file.
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.787 seconds) |
Compare pre and post base-quality scores from recalibration
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:13 (1.387 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.028 seconds) |
| Inputs |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:15 (1.483 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:15 - 2016-5-16 11:17:41 (25.368 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21384 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:41 - 2016-5-16 11:26:6 (8 minutes, 25.224 seconds) |
| Inputs |
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| Commands | 21637 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:26:6 (0.033 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:26:6 (0.008 seconds) |
Branch 146
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.792 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 (0.838 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.694 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 (0.563 seconds) |
| Inputs |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:43 (25.130 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (24.094 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.766 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.854 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.721 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.729 seconds) |
Compare pre and post base-quality scores from recalibration
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.322 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 (0.926 seconds) |
| Inputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.464 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:15 - 2016-5-16 11:17:42 (27.585 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21453 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:42 - 2016-5-16 11:35:39 (17 minutes, 56.379 seconds) |
| Inputs |
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| Commands | 21850 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:35:39 (0.036 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:35:39 (0.010 seconds) |
Branch 147
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (19.941 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.123 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (23.109 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:20 (1.960 seconds) |
| Inputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:20 - 2016-5-16 11:16:48 (28.014 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:48 - 2016-5-16 11:17:9 (21.156 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.973 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:10 (0.468 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.606 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 (0.829 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 (0.892 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:15 (1.910 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:15 - 2016-5-16 11:17:18 (2.220 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:18 - 2016-5-16 11:17:45 (27.394 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21428 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:45 - 2016-5-16 11:32:31 (14 minutes, 45.902 seconds) |
| Inputs |
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| Commands | 21787 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:32:31 (0.036 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:32:31 (0.007 seconds) |
Branch 148
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.569 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.220 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:19 (23.270 seconds) |
Create merged BAM alignment from unmapped BAM file
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:20 (1.392 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:20 - 2016-5-16 11:16:44 (23.919 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.687 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.661 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.318 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
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| Execution Time | 2016-5-16 11:17:9 (0.794 seconds) |
Apply BQSR to input BAM file.
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.713 seconds) |
Compare pre and post base-quality scores from recalibration
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.478 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 (0.999 seconds) |
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| Outputs |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.260 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:40 (26.631 seconds) |
Collect insert size metrics
| Inputs |
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| Commands | 21365 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:41 - 2016-5-16 11:22:56 (5 minutes, 15.232 seconds) |
| Inputs |
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| Commands | 21571 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:22:56 (0.069 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
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| Outputs |
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| Execution Time | 2016-5-16 11:22:56 (0.009 seconds) |
Branch 149
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (20.477 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.148 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.665 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Execution Time | 2016-5-16 11:16:18 (0.711 seconds) |
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| Outputs |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:44 (25.623 seconds) |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.270 seconds) |
Mark Duplicates with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.758 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.738 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.916 seconds) |
Apply BQSR to input BAM file.
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.398 seconds) |
Compare pre and post base-quality scores from recalibration
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|---|---|
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.991 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 (0.912 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 (0.533 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:40 (26.614 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21411 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:40 - 2016-5-16 11:30:5 (12 minutes, 24.350 seconds) |
| Inputs |
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|---|---|
| Commands | 21727 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:30:5 (0.040 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:30:5 (0.009 seconds) |
Branch 150
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Outputs |
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.917 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.119 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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|---|---|
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| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.898 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:20 (1.323 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:20 - 2016-5-16 11:16:44 (24.755 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (24.055 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.818 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.352 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.742 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.921 seconds) |
Compare pre and post base-quality scores from recalibration
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.027 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.027 seconds) |
| Inputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:16 (1.673 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:16 - 2016-5-16 11:17:43 (27.851 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21436 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:44 - 2016-5-16 11:33:8 (15 minutes, 24.244 seconds) |
| Inputs |
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|---|---|
| Commands | 21793 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:33:8 (0.034 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:33:8 (0.010 seconds) |
Branch 151
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
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| Outputs |
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| Execution Time | 2016-5-16 11:15:34 - 2016-5-16 11:15:54 (19.991 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.299 seconds) |
Mark Illumina Adapters with PicardTools
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| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (22.693 seconds) |
Create merged BAM alignment from unmapped BAM file
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:19 (1.449 seconds) |
| Inputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:19 - 2016-5-16 11:16:45 (26.171 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:45 - 2016-5-16 11:17:9 (23.237 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.651 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:9 (0.689 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.579 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 - 2016-5-16 11:17:12 (1.096 seconds) |
Compare pre and post base-quality scores from recalibration
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 - 2016-5-16 11:17:13 (1.050 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 (0.987 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:15 (1.293 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:15 - 2016-5-16 11:17:42 (26.100 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21382 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:42 - 2016-5-16 11:27:7 (9 minutes, 25.595 seconds) |
| Inputs |
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|---|---|
| Commands | 21652 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:27:7 (0.033 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:27:7 (0.012 seconds) |
Branch 152
Create uBAM from input BAM file using revert sam. Note we clean bam (revert mapQ=0 for unmapped reads) file before reverting.
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:15:33 - 2016-5-16 11:15:54 (20.623 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:15:54 - 2016-5-16 11:15:55 (1.216 seconds) |
Mark Illumina Adapters with PicardTools
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:15:55 - 2016-5-16 11:16:18 (23.026 seconds) |
Create merged BAM alignment from unmapped BAM file
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:18 - 2016-5-16 11:16:20 (1.481 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:20 - 2016-5-16 11:16:44 (24.041 seconds) |
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:16:44 - 2016-5-16 11:17:8 (23.533 seconds) |
Mark Duplicates with PicardTools
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.873 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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| Commands | |
| Outputs |
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| Execution Time | 2016-5-16 11:17:8 (0.657 seconds) |
Recalibrate base qualities in a BAM file so that quality metrics match actual observed error rates
| Inputs |
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|---|---|
| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:9 (0.685 seconds) |
Apply BQSR to input BAM file.
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:10 (0.870 seconds) |
Compare pre and post base-quality scores from recalibration
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:11 (0.842 seconds) |
Run FASTQC to generate QC metrics for the reads post-alignment
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:12 (0.896 seconds) |
| Inputs |
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| Commands | |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:17:13 - 2016-5-16 11:17:14 (1.273 seconds) |
Collect alignment summary statistics
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| Outputs |
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| Execution Time | 2016-5-16 11:17:14 - 2016-5-16 11:17:40 (25.876 seconds) |
Collect insert size metrics
| Inputs |
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|---|---|
| Commands | 21417 |
| Outputs |
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| Execution Time | 2016-5-16 11:17:40 - 2016-5-16 11:31:11 (13 minutes, 30.869 seconds) |
| Inputs |
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|---|---|
| Commands | 21748 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:31:11 (0.033 seconds) |
Call SNPs/SNVs using GATK Haplotype Caller, produces .g.vcf
| Inputs |
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| Outputs |
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| Execution Time | 2016-5-16 11:31:11 (0.007 seconds) |
Branch 153
Jointly genotype gVCF files
| Inputs |
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| Execution Time | 2016-5-16 11:40:20 (0.070 seconds) |
Generate variant quality score recalibration. Note requires GATK version 3.5
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:40:20 (0.005 seconds) |
Apply variant quality score recalibration
| Inputs |
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| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:40:20 (0.004 seconds) |
Annotate variants using snpEff
| Inputs |
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| Commands | 21940 |
| Outputs |
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| Execution Time | 2016-5-16 11:40:20 - 2016-5-16 11:45:57 (5 minutes, 37.667 seconds) |
Include core regions from Pf genetic crosses version 1
| Inputs |
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|---|---|
| Commands | 21941 |
| Outputs |
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| Execution Time | 2016-5-16 11:45:57 - 2016-5-16 11:48:48 (2 minutes, 50.630 seconds) |
Annotate global barcode SNPs from Neafsey et al., 2008
| Inputs |
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|---|---|
| Commands | 21942 |
| Outputs |
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| Execution Time | 2016-5-16 11:48:48 - 2016-5-16 11:50:50 (2 minutes, 1.442 seconds) |
Kepp only SNPs in VCF file
| Inputs |
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| Commands | 21943 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:50:50 - 2016-5-16 11:52:51 (2 minutes, 1.597 seconds) |
Annotate VCF file with additional filters at the variant level
| Inputs |
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|---|---|
| Commands | 21945 |
| Outputs |
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| Tools |
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| Execution Time | 2016-5-16 11:52:51 - 2016-5-16 11:53:27 (36.010 seconds) |
Clean VCF for analysis ready.
| Inputs |
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|---|---|
| Commands | 21947 |
| Outputs |
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| Execution Time | 2016-5-16 11:53:27 - 2016-5-16 11:53:47 (20.183 seconds) |
Use snpSift to extract annotations as plain text file
| Inputs |
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|---|---|
| Commands | 21949 |
| Outputs |
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| Execution Time | 2016-5-16 11:53:47 - 2016-5-16 11:53:52 (4.831 seconds) |
| Inputs |
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|---|---|
| Commands | 21951 |
| Outputs |
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| Execution Time | 2016-5-16 11:53:52 - 2016-5-16 11:57:26 (3 minutes, 33.700 seconds) |
Use clean VCF to construct GDS file
| Inputs |
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| Commands | 21952 |
| Outputs |
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| Execution Time | 2016-5-16 11:57:26 - 2016-5-16 11:58:53 (1 minutes, 27.378 seconds) |